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.     

Conformational preferences of proline oligopeptides

A conformational study on the terminally blocked proline oligopeptides, Ac-(Pro)(n)()-NMe(2) (n = 2-5), is carried out using the ab initio Hartree-Fock level of theory with the self-consistent reaction field method in the gas phase and in solutions (chloroform, 1-propanol, and water) to explore the preference and transition between polyproline II (PPII) and polyproline I (PPI) conformations depending on the chain length, the puckering, and the solvent. The mean differences in the free energy per proline of the up-puckered conformations relative to the down-puckered conformations for both diproline and triproline increases for the PPII-like conformations and decreases for the PPI-like conformations as the solvent polarity increases. These calculated results indicate that the PPII-like structures have preferentially all-down puckerings in solutions, whereas the PPI-like structures have partially mixed puckerings. The free energy difference per proline residue between the PPII- and PPI-like structures decreases as the proline chain becomes longer in the gas phase but increases as the proline chain becomes longer in solutions and the solvent polarity increases. In particular, our calculated results indicate that each of the proline oligopeptides can exist as an ensemble of conformations with the trans and cis peptide bonds in solutions, although the PPII-like structure with all-trans peptide bonds is dominantly preferred, which is reasonably consistent with the previously observed results. In diproline Ac-(Pro)(2)-NMe(2), the rotational barrier to the cis-to-trans isomerization for the first prolyl peptide bond increases as the solvent polarity increases, whereas the rotational barrier for the second prolyl peptide bond does not show the monotonic increase as the solvent polarity increases. When the rotational barriers for these two prolyl peptide bonds were compared, it could be deduced that the conformational transition from PPI with the cis peptide bond to PPII with the trans peptide bond is initiated at the C-terminus and proceeds to the N-terminus in water. This is consistent with the results from NMR experiments on polyproline in D(2)O but opposite to the results from enzymatic hydrolysis kinetics experiments on polyproline.     

Conformational manifold of alpha-aminoisobutyric acid (Aib) containing alanine-based tripeptides in aqueous solution explored by vibrational spectroscopy, electronic circular dichroism spectroscopy, and molecular dynamics simulations

Replacement of the alpha-proton of an alanine residue to generate alpha-aminoisobutyric acid (Aib) in alanine-based oligopeptides favors the formation of a 3(10) helix when the length of the oligopeptide is about four to six residues. This research was aimed at experimentally identifying the structural impact of an individual Aib residue in an alanine context of short peptides in water and Aib's influence on the conformation of nearest-neighbor residues. The amide I band profile of the IR, isotropic and anisotropic Raman, and vibrational circular dichroism (VCD) spectra of Ac-Ala-Ala-Aib-OMe, Ac-Ala-Aib-Ala-OMe, and Ac-Aib-Ala-Ala-OMe were measured and analyzed in terms of different structural models by utilizing an algorithm that exploits the excitonic coupling between amide I' modes. The conformational search was guided by the respective 1H NMR and electronic circular dichroism spectra of the respective peptides, which were also recorded. From these analyses, all peptides adopted multiple conformations. Aib predominantly sampled the right-handed and left-handed 3(10)-helix region and to a minor extent the bridge region between the polyproline (PPII) and the helical regions of the Ramachandran plot. Generally, alanine showed the anticipated PPII propensity, but its conformational equilibrium was shifted towards helical conformations in Ac-Aib-Ala-Ala-OMe, indicating that Aib can induce helical conformations of neighboring residues positioned towards the C-terminal direction of the peptide. An energy landscape exploration by molecular dynamics simulations corroborated the results of the spectroscopic studies. They also revealed the dynamics and pathways of potential conformational transitions of the corresponding Aib residues.     

Convergent Synthesis of Repeating Peptides (Val-X-Leu-Pro-Pro-Pro)(8) Adopting a Polyproline II Conformation

The N-terminal domain of maize gamma-zein has a repetitive structure (Val-His-Leu-Pro-Pro-Pro)(8) that has recently been shown to adopt an amphipathic polyproline II type conformation in aqueous solution. We report here the synthesis and conformational analysis of three model peptides (Val-X-Leu-Pro-Pro-Pro)(8) (X = Ala (1), Glu (2), Lys (3)). The three compounds have been synthesized in a very efficient way using a convergent solid-phase strategy. Circular dichroism shows unequivocally that the three model peptides adopt polyproline II (PPII) type conformations under a variety of experimental conditions and that neither the presence of histidine nor amphipathicity of the peptide is an absolute requirement for adopting the native conformation. These results open the door for the de novo design of compounds with PPII conformations and must be taken into account in the structure prediction of protein structures from sequence data banks.     

Uni‐molecular nanoparticles of poly(2‐oxazoline) showing tunable thermoresponsive behaviors

Herein, cylindrical molecular bottlebrushes grafted with poly(2‐oxazoline) (POx) as a shaped tunable uni‐molecular nanoparticle were synthesized via the grafting‐onto approach. First, poly(glycidyl methacrylate) (PGMA) backbones with azide pendant units were prepared via reversible addition fragmentation transfer (RAFT) polymerization followed by post‐modification. The degree of polymerization (DP) of the backbones was tuned in a range from 20 to 800. Alkynyl‐terminated POx side chains were synthesized by living cationic ring opening polymerization (LCROP) of 2‐ethyl‐2‐oxazoline (EtOx) and 2‐methyl‐2‐oxazoline (MeOx), respectively. The DP of side chains was varied between 20 and 100. Then, the copper‐catalyzed azide‐alkynyl cycloaddition (CuAAC) click chemistry was conducted with a feed ratio of [alkynyl]:[azide] = 1.2:1 to yield a series of brushes. Depending on the DP of side chains, the grafting density ranged between 47 and 85%. The resulting brushlike nanoparticles exhibited shapes of sphere, rod and worm. Aqueous solutions of PEtOx brushes demonstrated a thermoresponsive behavior as a function of the length of backbones and side chains. Surprisingly, it was found that the lower critical solution temperature of PEtOx brushes increased with a length increase of backbones. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2018 , 56, 174–183     

Helical Folding of Conjugated Oligo(phenyleneethynylene): Chain‐Length Dependence,Solvent Effects,and Intermolecular Assembly

As a representative folding system that features a conjugated backbone, a series of monodispersed (o‐phenyleneethynylene)‐alt‐(p‐phenyleneethynylene) (PE) oligomers of varied chain length and different side chains were studied. Molecules with the same backbone but different side‐chain structures were shown to exhibit similar helical conformations in respectively suitable solvents. Specifically, oligomers with dodecyloxy side chains folded into the helical structure in apolar aliphatic solvents, whereas an analogous oligomer with tri(ethylene glycol) (Tg) side chains adopted the same conformation in polar solvents. The fact that the oligomers with the same backbone manifested a similar folded conformation independent of side chains and the nature of the solvent confirmed the concept that the driving force for folding was the intramolecular aromatic stacking and solvophobic interactions. Although all were capable of inducing folding, different solvents were shown to bestow slightly varied folding stability. The chain‐length dependence study revealed a nonlinear correlation between the folding stability with backbone chain length. A critical size of approximately 10 PE units was identified for the system, beyond which folding occurred. This observation corroborated the helical nature of the folded structure. Remarkably, based on the absorption and emission spectra, the effective conjugation length of the system extended more effectively under the folded state than under random conformations. Moreover, as evidenced by the optical spectra and dynamic light‐scattering studies, intermolecular association took place among the helical oligomers with Tg side chains in aqueous solution. The demonstrated ability of such a conjugated foldamer in self‐assembling into hierarchical supramolecular structures promises application potential for the system.     

Intrinsically cell-permeable miniature proteins based on a minimal cationic PPII motif

Cell-penetrating peptides (CPPs) provide promising tools for the cellular delivery of molecular cargos ranging in size from small molecules and peptides to proteins and quantum dots. CPPs are typically cationic and/or amphipathic sequences that are unstructured or alpha-helical. We expand the repertoire of cell-penetrating motifs by designing encodable CPPs possessing type-II polyproline (PPII) helical structure. These motifs surpass the uptake efficiency of existing CPPs and are not cytotoxic at concentrations 100 times greater than that necessary for delivery. By replacing the PPII helix of a miniature protein, the motif can endow intrinsic cell permeability without increasing molecular size.     

Water-Soluble Polypeptides with Elongated, Charged Side Chains Adopt Ultra-Stable Helical Conformations

Water-soluble polypeptides adopting α-helical conformations with unprecedented high helicities were obtained by elongating the charge-containing side chains of the constituent amino acids to allow the terminal charges to be situated distally from the peptide backbone. Poly(γ-(4-aminoethylthiopropoxyl)-benzyl-(L)-glutamate) (PAOBLG-AET) with a charge-peptide backbone distance of 17 σ-bonds exhibited a remarkably high helical content (81%) at a degree of polymerization as low as 10. The helical conformations of these short polypeptides were very stable against various harsh, protein-denaturing conditions, such as extreme pH, high temperature, and high salt or urea concentrations.     

Molecular Bottlebrushes with Polypeptide Backbone Prepared via Ring‐Opening Polymerization of NCA and ATRP

A new type of molecular bottlebrush with poly‐L ‐lysine (PLL) as backbone was synthesized via ROP followed by ATRP. A Nϵ‐bromoisobutyryl functionalized Nα‐CBZ‐L ‐lysine was firstly synthesized and converted in polymerizable α‐amino acid N‐carboxyanhydride (NCA), which was then polymerized using Ni(0) transition metal complex to give well‐defined bromo‐functionalized homopolypeptide (PBrLL), from which we prepared two types of polypeptide bottlebrushes with polystyrene and poly(oligoethylene glycol methacrylate) as side‐chains. PBrLL macroinitiator was demonstrated to have high initiation efficiency for ATRP, which allowed good control over side‐chain length. CD and FTIR characterization revealed that both PBrLL macroinitiator and PLL backbone of bottlebrushes adopted α‐helical conformation in appropriate solvents.     

Morphology study of Nafion membranes prepared by solutions casting

The structures of Nafion membranes prepared by solutions casting from low aliphatic alcohols/water mixture solvents and N,N′‐dimethyl formamide (DMF) solvent were investigated using differential scanning calorimeter and small angle X‐ray scattering. The aggregation behavior of Nafion molecules in the casting solutions was also investigated using dynamic light scattering. We show that the morphology of membranes was strongly influenced by the conformations of Nafion molecules in the solutions. In aliphatic alcohol/water mixture solvents, which have a worse compatibility with Nafion backbones, the Nafion molecules aggregate and form fringed rod‐like structures. These primary rod‐like structures then aggregate again through fringed side chains to form secondary ionic aggregations. In DMF solvent, owing to its better compatibility with Nafion backbones, less Nafion molecules aggregate. The high degree of Nafion molecular aggregations in aliphatic alcohol/water mixture solvents leads to a high degree of hydrophobic and hydrophilic phase separation for membranes prepared by casting from Nafion/aliphatic alcohol/water solutions. However, the lower degree of molecular aggregations in DMF solvent results in a lower degree of hydrophobic and hydrophilic phase separation for membranes prepared by casting from Nafion/DMF solution. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 3044–3057, 2005     

Demonstration of the ring conformation in polyproline by the Raman optical activity

Raman and Raman optical activity (ROA) spectra of poly-L-proline were recorded in a wide frequency range and analyzed with respect to the proline side chain conformation. The analysis was based on comparison to ab initio simulations of spectral band positions and intensities. The presence of two conformer states of the five-member ring was found, approximately equally populated in the polypeptide. Additionally, Raman and ROA spectral shapes indicated that the peptide adopts the polyproline II helical conformation, in both aqueous and TFE solutions. The helix, however, is perturbed by fluctuations, which affects the vibrational coupling among amino acid residues and broadens the ROA bands. Contributions of the side and main peptide chains to the polyproline ROA intensities have comparable magnitudes. Thus understanding of the origins of both signals is important for determination of the peptide structure by ROA.     

Thermoresponsive Dendronized Polyprolines via the “Grafting to” Route

The first and second generations of dendronized polyprolines P3G1 , P3G2, and P4G1 are prepared via the “grafting to” route, and their thermoresponsive properties and helical conformations investigated. High molar masses of polyproline main chains carrying azido groups are achieved first by polycondensation of peptide precursors through activated ester strategy. Oligoethylene glycol dendrons cored with alkyne are then attached onto the main chains through click reaction. These polymers are found to be thermoresponsive. Circular dichroism spectroscopy investigation indicates, in contrast to P3G2 and P4G1 which adopt the expected PPII conformation in aqueous conditions, P3G1 prefers to adopt PPI helical conformation, and this conformation is stable within the measured time period and temperature range.

     

UV Raman demonstrates that alpha-helical polyalanine peptides melt to polyproline II conformations

We examined the 204-nm UV Raman spectra of the peptide XAO, which was previously found by Shi et al.'s NMR study to occur in aqueous solution in a polyproline II (PPII) conformation. The UV Raman spectra of XAO are essentially identical to the spectra of small peptides such as ala(5) and to the large 21-residue predominantly Ala peptide, AP. We conclude that the non-alpha-helical conformations of these peptides are dominantly PPII. Thus, AP, which is highly alpha-helical at room temperature, melts to a PPII conformation. There is no indication of any population of intermediate disordered conformations. We continued our development of methods to relate the Ramachandran Psi-angle to the amide III band frequency. We describe a new method to estimate the Ramachandran Psi-angular distributions from amide III band line shapes measured in 204-nm UV Raman spectra. We used this method to compare the Psi-distributions in XAO, ala(5), the non-alpha-helical state of AP, and acid-denatured apomyoglobin. In addition, we estimated the Psi-angle distributions of peptide bonds which occur in non-alpha-helix and non-beta-sheet conformations in a small library of proteins.     

Conformational behavior of polymers adsorbed on nanotubes

The importance of hydrophobic interactions in determining polymer adsorption and wrapping of carbon nanotubes is still under debate. In this work, we concentrate on the effect of short-ranged weakly attractive hydrophobic interactions between polymers and nanotubes (modeled as an infinitely long and smooth cylindrical surface), neglecting all other interactions apart for chain flexibility. Using coarse-grained Monte Carlo simulation of such simplified systems, we find that uniform adsorption and wrapping of the nanotube occur for all degrees of chain flexibility for tubes with sufficiently large outer radii. However, the adsorbed conformations depend on chain stiffness, ranging from randomly adsorbed conformations of the flexible chain to perfect helical or multihelical conformations (in the case of more concentrated solutions) of the rigid chains. Adsorption appears to occur in a sequential manner, wrapping the nanotube nearly one monomer at a time from the point of contact. Once adsorbed, the chains travel on the surface of the cylinder, retaining their helical conformations for the semiflexible and rigid chains. Our findings may provide additional insight to experimentally observed ordered polymer wrapping of carbon nanotubes.     

A Reversibly Porous Supramolecular Peptide Framework**

The ability to use bio-inspired building blocks in the assembly of novel supramolecular frameworks is at the forefront of an exciting research field. Herein, we present the first polyproline helix to self-assemble into a reversibly porous, crystalline, supramolecular peptide framework (SPF). This framework is assembled from a short oligoproline, adopting the polyproline II conformation, driven by hydrogen-bonding and dispersion interactions. Thermal activation, guest-induced dynamic porosity and enantioselective guest inclusion have been demonstrated for this novel system. The principles of the self-assembly associated with this SPF will be used as a blueprint allowing for the further development of helical peptide linkers in the rational design of SPFs and metal-peptide frameworks.     

以聚乳酸为侧链的光学活性聚苯乙炔的合成与表征

通过4-溴苯甲醇和三甲基硅基乙炔的Sonagashira偶联反应与三甲基硅基的脱除反应,合成4-乙炔基苯甲醇.以4-乙炔基苯甲醇为引发剂,以有机氮杂环化合物DBU为催化剂,常温常压下进行丙交酯的活性开环聚合反应,采用1H-NMR和GPC对产物结构、分子量与分子量分布进行表征分析,结果表明,合成以了苯乙炔为端基的聚乳酸大...     

UV resonance Raman determination of polyproline II, extended 2.5(1)-helix, and beta-sheet Psi angle energy landscape in poly-L-lysine and poly-L-glutamic acid

UV resonance Raman (UVR) spectroscopy was used to examine the solution conformation of poly-l-lysine (PLL) and poly-l-glutamic acid (PGA) in their non-alpha-helical states. UVR measurements indicate that PLL (at pH = 2) and PGA (at pH = 9) exist mainly in a mixture of polyproline II (PPII) and a novel left-handed 2.5(1)-helical conformation, which is an extended beta-strand-like conformation with Psi approximately +170 degrees and Phi approximately -130 degrees . Both of these conformations are highly exposed to water. The energies of these conformations are very similar. We see no evidence of any disordered "random coil" states. In addition, we find that a PLL and PGA mixture at neutral pH is approximately 60% beta-sheet and contains PPII and extended 2.5(1)-helix conformations. The beta-sheet conformation shows little evidence of amide backbone hydrogen bonding to water. We also developed a method to estimate the distribution of Psi Ramachandran angles for these conformations, which we used to estimate a Psi Ramachandran angle energy landscape. We believe that these are the first experimental studies to give direct information on protein and peptide energy landscapes.