Polypeptide Secondary Structure Research Articles

Position Matters: Pyridine Regioisomers Influence Secondary Structure and Micelle Morphology in Polymer-Homopolypeptide Micelles.

Polymer-homopolypeptide block copolymers are a class of bioinspired materials that combine the processability and stability of synthetic polymers with the biocompatibility and unique secondary structures of peptides, such as α-helices and β-sheets. These properties make them ideal candidates for a wide variety of applications, for example, in the pharmaceutical field, where they are frequently explored as building blocks for polymeric micelle drug delivery systems. While homopolypeptide side chains can be furnished with an array of different moieties to impart the copolymers with desirable properties, such as stimulus responsivity, pyridine derivatives represent an underutilized functional group for this purpose. Additionally, the interplay between polypeptide side chain structure, secondary conformation, and micelle morphology is not yet well understood, particularly in the case of structural regioisomers. Therefore, in this work, a series of polymer-homopolypeptide copolymers were prepared from a poly(ethylene glycol)-b-poly(glutamic acid) (PEG-b-PGA) backbone, where the pendant carboxylic acid groups were covalently conjugated to a series of pyridine regioisomers by carbodiimide coupling. These pyridine regioisomers differed only in the position of the nitrogen heteroatom, ortho, meta or para, relative to the linking group, generating a series of PEG-b-poly(pyridinylmethyl glutamate) (PEG-b-PMG) copolymers. Following self-assembly of the copolymers in aqueous solutions, dynamic light scattering (DLS) revealed differences in micelle hydrodynamic diameter (Dh) (ranging from ∼60 to 120 nm), while transmission electron microscopy (TEM) and small-angle X-ray scattering (SAXS) revealed distinctive morphologies ranging from ellipsoidal, to cylindrical, and disc-like, suggesting that subtle changes in positional isomers in the polypeptide block may influence the micelle structure. Analysis of the PEG-b-PMG copolymer micelles by circular dichroism (CD) and attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy revealed that differences in the morphology were associated with changes in polypeptide secondary structure, which in turn was influenced by the position of the pyridine heteroatom. Overall, these findings contribute to the broader understanding of the relationship between polypeptide structure and micelle morphology and serve as useful insight for the rational design of polymer-polypeptide nanoparticles.

Characterization of Secondary Structures of Model Polypeptides in Solutions with Hyper-Raman Spectroscopy.

Characterization of the secondary structures of two model polypeptides, poly-l-lysine and poly-l-glutamic acid in aqueous solutions has been demonstrated by hyper-Raman (HR) spectroscopy for the first time. Complementary to infrared (IR) and visible Raman spectroscopy, HR spectroscopy gives the amide I, II, and III bands originating from the polypeptide backbones and the CCH3 symmetric bending mode, enabling us to distinguish different conformations. The α-helix gives the broad and weak amide III band, while the β-sheet and the random coil show similar spectral patterns with different relative intensities between the amide I and II bands. HR spectra from aqueous solutions of the α-helix and the random coil of poly-l-ornithine also possess these spectral features. The HR spectra are analogous to UV resonance Raman (UVRR) spectra, indicating the signal enhancement due to the electronic resonance effect via the π-π* transition. In contrast, the vibrational frequencies of the amide I band in the HR spectra are much higher than those in the IR, visible Raman, and UVRR spectra, suggesting the non-coincidence between HR, IR, and Raman bands. Our finding suggests that HR spectroscopy is promising to provide complementary information on the secondary structures of polypeptides in aqueous solutions as a spectral approach differing from existing vibrational spectroscopic methods.

Secondary Structure-Governed Phase Separation Behavior in Glutamate-Based Polypeptides.

The phase separation behavior of biomacromolecules plays a key role in the fields of biology and medicine. In this work, we gain a deep insight into how the primary and secondary structures govern and regulate the phase separation behavior of polypeptides. To this end, we synthesized a series of polypeptides with tailorable hydroxyl-containing side chains. The secondary structure of polypeptides can be modulated by the local chemical environment and content of side chains. Interestingly, these polypeptides with different helical contents exhibited upper critical solution temperature behavior with marked differences in the cloud point temperature (Tcp) and the width of hysteresis. The phase transition temperature is highly relevant to the content of secondary structure and interchain interactions of polypeptides. The aggregation/deaggregation and the transition of secondary structure are completely reversible during heating-cooling cycles. Much to our surprise, the recovery rate of the α-helical structure governs the width of hysteresis. This work establishes the structure-property relationship between the secondary structure and phase separation behavior of the polypeptide and delivers new insight into the rational design of peptide-based materials with tailor-made phase separation behavior.

Theoretical study on spectral differences of polypeptides constituted by L- and D-amino acids

Amino acids, polypeptides and proteins, which are all chiral, are the most important living substances. Most living organisms are made up of L-amino acids. Chirality is of great significance in exploring biomolecules. Studying polypeptides with a large number of atoms is a great challenge for quantum chemistry calculation. We conduct structural studies and perform vibrational and electronic spectra investigations on two polypeptides consisting of 14 L- and D-amino acids, both of which are right-handed α-helical. We find that the two polypeptides have similar IR and Raman vibrational spectra except that the polypeptide constituted by D-amino acids has an intramolecular hydrogen bond peak, but their chiral and excited state spectra are different and the chiral spectra are not mirror symmetric, which can be applied to distinguish them and shows that they have different structures in detail. Thus they may have different properties and functions. In addition, the amide III vibrations of the polypeptide include the information of the backbone and side chains. Therefore, care should be taken to apply the amide III vibrations to determine the secondary structure of polypeptide.

Development of a Negative-Biased Zwitterionic Polypeptide-Based Nanodrug Vehicle for pH-Triggered Cellular Uptake and Accelerated Drug Release.

Albumin mimics could be an attractive platform for nanodrug carriers through systematic administration because of high safety and plentiful properties to be adjusted for a high drug efficacy, such as pH-triggered targeting cellular uptake and drug release. In this work, negative-biased zwitterionic nanodrug carriers based on zwitterionic polypeptide chains that mimic albumin were prepared, which have an outermost layer of zwitterionic glutamic acid (E) and lysine (K) pairs with a small amount of aspartic acid (D) to adjust the overall ζ potential. On the other hand, doxorubicin (Dox) was encapsulated in a hydrophobic core by 11-maleimidoundecanoic acid covalently linked with additional cysteine (C) residues on the polypeptide. The results show that the negative-biased zwitterionic nanodrug carriers can sensitively enhance the cellular uptake in responding to a pH change from 7.4 to 6.7 without reversing the ζ potential to a positive charge, leading to accelerating the Dox release rate in a slightly acidic environment through the polypeptide secondary structure change. Moreover, the anionic nanodrug carrier can also be easily enzymatically digested by trypsin for quick drug release. In short, this negative-biased zwitterionic nanodrug delivery vector could be an ideal candidate for a safer tumor inhibition with a high efficacy than conventional synthetic polymer-based ones.

Effect of polypeptide block length on nano-assembly morphology and thermo-sensitivity of methyl poly (ethylene glycol)-poly (L-valine) copolymer aqueous solutions

The delicacy of nature prompted scientists to create functional or responsive biomaterials using existing natural components. Here we reported novel thermo-gelling hydrogels based on methyl poly (ethylene glycol)-poly (L-valine) (mPEG-L-PV) diblock copolymer solutions, which exhibited well-defined sol–gel transition at a temperature range from 10 °C to 40 °C. The β-sheet was the dominant secondary structure for poly(L-PV) block when the molecular weight of the polypeptide ranged from 277 Da to 1138 Da. The formation of mPEG–L-PV clear sol solutions was related to the stable nanostructures that were aggregated clusters of poly(L-PV) β-sheet filaments and stabilized by the hydrophilic PEG segments. The block length of poly(L-PV) significantly affected the secondary structures of polypeptide and the morphology of assembled filaments, which resulted in different thermo-gelling behavior of the copolymer solutions. The occurrence of sol–gel transition with temperature was primarily due to the dehydration effect of PEG block, whereas in the case of the copolymer with a lower molecular weight of poly(L-PV) block, the change of polypeptide secondary structures also contributed to the formation of the gel. This paper provides fundamental information about the strong dependence of polypeptide block length on the nano-assembly morphology as well as thermosensitive behavior of polypeptide-based hydrogels.

Synthesis of AIE polyethylene glycol-block-polypeptide bioconjugates and cell uptake assessments of their self-assembled nanoparticles

A synthetic polypeptide-based bioconjugate bearing tetraphenylethylene (TPE) at the polypeptide side chains, named mPEG-PPLGgTPE, was synthesized by ring-opening polymerization (ROP) of α-amino acid-N-carboxyanhydride (NCA) along with post-polymerization modification method. Interestingly, the bioconjugate enabled both the aggregation induced emission (AIE) effect at 469 nm and the aggregation caused quenching (ACQ) effect around 365 nm depending on water fraction in the tetrahydrofuran/water (THF/H2O) mixed solution, and this feature was very different from the commonly used TPE-based AIE polymers. The strong emission at the 365 nm was a rarely seen monomeric emission for the TPE units. Further studies on the fluorescence spectra indicated that the monomeric emission was not related with the secondary structure of polypeptides, but caused by the TPE unit itself. The mPEG-PPLGgTPE could self-assemble to AIE nanoparticles (NPs) in water in a mean size of 253 nm with polyethylene glycol (PEG) as the shells in surface. In addition, HeLa cell uptake level of the NPs was unsatisfactory according to the cell imaging results, which was independent of the polypeptides conformation, the PEG length and the size of NPs.

Peptidomic analysis of hydrolyzed oat bran proteins, and their in vitro antioxidant and metal chelating properties

Peptide profiles of hydrolyzed oat proteins and the susceptibility of their polypeptides to proteolytic cleavages were determined using peptidomic analysis. In addition, antioxidant activities were also measured. Proteins isolates were first extracted with carbohydrases, Viscozyme or Cellulase and then hydrolyzed with proteases (Alcalase, Papain, Protamex, Flavourzyme). Amongst the eight hydrolysates, Viscozyme-proteins hydrolyzed with Papain showed the highest ability to quench ABTS+ radicals (866.9 ± 10.6 µM TE/g) and to chelate ferrous ions (75 ± 0.4%) while displaying the second strongest activity for ROO radicals (396.7 ± 14.0 µM TE/g). Peptidomics analysis showed that the higher activity of papain hydrolysate in most assays was related to its greater proteolytic action on main proteins (avenin, 11S- and 12S-globulins) compared to other proteases. In addition, the number of peptides identified in the Papain digest of proteins extracted with Viscozyme was about half relative to the number in proteins from bran treated with Cellulase and digested with the same protease. This was likely because the carbohydrases differently affected polypeptide secondary structures.

Secondary structures of synthetic polypeptide polymers

Synthetic peptide-based polymers can fold into different secondary structures in the same way as do proteins. This review article presents how tuning the polypeptide secondary structure could be a key step to modulate various properties in advanced polymeric materials (size, rigidity, self-assembly,etc.).

Synthesis and gelation of copolypept(o)ides with random and block structure.

Copolypept(o)ides of polysarcosine (PSar) and poly(N-isopropyl-L-glutamine) (PIGA) with random and block sequence structures were synthesized by ring-opening polymerization (ROP) of sarcosine N-carboxyanhydrides (Sar-NCA) and γ-benzyl-l-glutamate N-carboxyanhydrides (BLG-NCA) and post modification. With different distribution of Sar along the main chain, H-bonding pattern and secondary structure of polypeptides were turned, as well as aggregation and gelation behavior. Both copolypept(o)ides formed hydrogels above their critical gelation concentrations (CGCs) without thermo-sensitivity, which was normally reserved for PEG copolypeptides (eg, PEG-b-PIGA). In particular, a different mechanism from previously reported micellar percolation or fibrillar entanglement was suggested for gelation of the random copolypept(o)ide. Therefore, hydrogels from copolymers of PSar and PIGA represented a new approach to construct easy-handling, biocompatible, biodegradable and thermo-stable gels that could potentially be applied in biomedical fields.

Conformational motion correlations in the formation of polypeptide secondary structure in a viscous medium

The Langevin dynamics method and statistical correlation analysis were used to study the α-helical structure folding dynamics of the (Ala)50, (AlaGly)25, and (AlaGly)75 polypeptides depending on the viscosity of the medium. Friction forces that arise when the effective viscosity of the medium is similar to the viscosity of water were found to result in strong correlations between the backbone torsion angles. The polypeptides under study folded mainly to produce α-helical structures. A structure of two contacting α-helices that were approximately equal in length and had a loop between them was observed for a longer chain of 150 residues. A method to visualize the correlation matrix of the dihedral angles of a polypeptide chain was developed for analyzing the effects of the dynamic correlation of conformational degrees of freedom. The analysis of the dynamics of the correlation matrix showed that rotations involving angles of the same type (φ–φ and ψ–ψ) occur predominantly in one direction. Rotations invoving different angles (φ–ψ) occur predominantly in opposite directions, so that the total macromolecule does not rotate. A significant reduction in the effective viscosity of the medium disrupts the correlation and makes the rotations stochastic, thus distorting the formation of the regular (helical) structure. The effects of correlated conformational motions are consequences of viscous friction forces. This conclusion agrees with our previous results that outlined the principle of the minimum rate of energy dissipation and the equipartition of energy dissipation rate between conformational degrees of freedom.

External cavity-quantum cascade laser infrared spectroscopy for secondary structure analysis of proteins at low concentrations.

Fourier transform infrared (FTIR) and circular dichroism (CD) spectroscopy are analytical techniques employed for the analysis of protein secondary structure. The use of CD spectroscopy is limited to low protein concentrations (<2 mg ml−1), while FTIR spectroscopy is commonly used in a higher concentration range (>5 mg ml−1). Here we introduce a quantum cascade laser (QCL)-based IR transmission setup for analysis of protein and polypeptide secondary structure at concentrations as low as 0.25 mg ml−1 in deuterated buffer solution. We present dynamic QCL-IR spectra of the temperature-induced α-helix to β-sheet transition of poly-L-lysine. The concentration dependence of the α-β transition temperature between 0.25 and 10 mg ml−1 was investigated by QCL-IR, FTIR and CD spectroscopy. By using QCL-IR spectroscopy it is possible to perform IR spectroscopic analysis in the same concentration range as CD spectroscopy, thus enabling a combined analysis of biomolecules secondary structure by CD and IR spectroscopy.

Aqueous Self-Assembly of a Protein-Mimetic Ampholytic Block Copolypeptide

This report describes the aggregation behavior of an ABC-type ampholytic block copolypeptide, poly(ethylene oxide)-block-poly(l-lysine)-block-poly(l-glutamate), in aqueous media in dependence of pH. Polypeptide secondary structures and self-assemblies are investigated by circular dichroism (CD), Fourier transform infrared (FT-IR) and NMR spectroscopy, zeta potential measurements, analytical ultracentrifugation (AUC), dynamic/static light scattering (DLS/SLS), and cryogenic transmission electron microscopy (cryo-TEM). The polymer chains tend to form vesicles when the hydrophobic polypeptide helix is located at the chain end (acidic pH) and are existing as single chains when it is located in the center and flanked by the two hydrophilic segments (basic pH). Precipitation occurs in the intermediate pH range due to polyion complexation of the charged polypeptide segments.

Thermoresponsive Dendronized Polypeptides Showing Switchable Recognition to Catechols

A new class of thermoresponsive dendronized polypeptides was prepared through highly efficient oxime ligation between oxyamino-substituted polylysines and aldehyde-cored oligoethylene glycol (OEG) dendrons. Their secondary structures and thermoresponsive behavior were investigated. Because of the dendritic structures and stable oxime linkage, these OEG-based dendronized polypeptides exhibited fast and fully reversible phase transitions in neutrally aqueous solutions, and their phase transition temperatures can be controlled around physiological temperatures. The effect of OEG dendronization on secondary structures of polypeptides were examined to check their prominent dendritic shielding effect, steric hindrance, and thermally driven phase transitions. To further extend the functions and potential applications of these stimuli-responsive dendronized polypeptides, phenylboronic acid moieties were introduced to achieve the corresponding dendronized copolymers, which were utilized to specifically recognize c...

Revealing graphene oxide toxicity mechanisms: A reactive molecular dynamics study

We report the first atomistic-scale study on graphene oxide (GO) toxicity, revealing potentially harmful chemical mechanisms of GO during its interactions with biomolecules. ReaxFF-based reactive molecular dynamics study was utilized to assess the impact of different functional groups on GO biocompatibility. Our study predicts different chemical reactions between the GO sheet and peptides that lead to reactive oxidative species (ROS), acidic or basic pHs and cell surface adhesions. We observe that cell-surface adhesion is a result of strong H-bonding and stable π–π stacking interaction. This stacking can also lead to the disruption of the polypeptide secondary structure.

Influence of secondary structure and hydrogen-bonding arrangement on the mechanical properties of peptidic-polyurea hybrids.

Bio-inspired materials design is an important strategy used in the fabrication of tunable and mechanically enhanced polymeric systems. An important aspect of bio-inspiration is to understand how components, such as hierarchy and self-assembly, affect the properties of the designed materials. In this investigation, we explore the use of polypeptide secondary structure and hydrogen bonding arrangement, in order to determine their effects on the thermal and mechanical properties of fully synthetic peptidic polyureas. Specifically, we incorporate either short β-sheet forming peptide blocks of poly(β-benzyl-l-aspartate)5 or poly(ε-carbobenzyloxy-l-lysine)5 or longer peptide blocks of poly(β-benzyl-l-aspartate)20 or poly(ε-carbobenzyloxy-l-lysine)20 as α-helix forming domains into non-chain extended polyureas based on 1,6-hexamethylene diisocyanate and poly(dimethysiloxane). Secondary structure was found to be influenced by the weight fraction of peptide, e.g. increasing peptide weight fractions increased sheet or helical ordering. Additionally, the polyurea microstructure was comprised of nanofibrils with a secondary structure dependent fiber width, attributed to the peptidic motif alignment within the nanothreads. Analysis of the thermomechanical and tensile response revealed multiple trends, such as increased toughness attributed to β-sheet ordering and increased modulus with increased peptide weight fraction. It is anticipated that this observed interplay between peptide organization and mechanics will be applicable to engineering and biomaterial development due to the simplicity of the synthetic protocol and the promising mechanical tunability guided by the peptide segment.

Stimuli‐responsive polypeptide materials prepared by ring‐opening polymerization of α‐amino acid N‐carboxyanhydrides

AbstractDesign and synthesis of biodegradable stimuli‐responsive polypeptides are important areas considering their promising applications in biomedical fields. This article summarizes the most recent progresses in the development of stimuli‐responsive polypeptide materials prepared via ring‐opening polymerization of α‐amino acid N‐carboxyanhydrides. We discuss the design, synthesis and structure‐property correlation of emerging materials including thermo‐responsive, redox‐responsive, photo‐responsive and biomolecule responsive polypeptides. Considering the unique structural features of amino acids, we try to emphasize that the thermo‐responsive properties not only depend on the amino acid structure but also rely on the secondary structures of polypeptides. © 2013 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2013

Molecular captain: A light-sensitive linker molecule in poly(ethylene glycol)-poly(L-alanine)-poly(ethylene glycol) triblock copolymer directs molecular nano-assembly, conformation, and sol-gel transition

We report a poly(ethylene glycol)-poly(L-alanine)-azobenzene-poly(L-alanine)-poly(ethylene glycol) (PEG-PA-Z-PA-PEG) as a temperature and light sensitive polymer. The poly(ethylene glycol)-poly(L-alanine) diblock copolymers with a flexible-rigid block structure were coupled by an azobenzene group that undergoes a reversible configurational change between “trans” and “cis” upon exposure to UV and vis light. The single azobenzene molecule embedded in the middle of a block copolymer with a flexible (shell)-rigid (core) structure significantly affected molecular assembly, micelle size, polypeptide secondary structure, and sol-to-gel transition temperature of the polymer aqueous solution, depending on its exposure to UV or vis light. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012

Helix versus coil polypeptide macromers: gel networks with decoupled stiffness and permeability.

As a platform for investigating the individual effects of substrate stiffness, permeability, and ligand density on cellular behavior, we developed a set of hydrogels with stiffness tuned by polymer backbone rigidity, independent of cross-link density and concentration. Previous studies report that poly(propargyl-L-glutamate) (PPLG), synthesized by ring-opening polymerization of the N-carboxy anhydride of γ-propargyl-L-glutamate (γpLglu), adopts a rigid a-helix conformation: we hypothesized that a random copolymer (PPDLG) with equal amounts of γpLglu and γ-propargyl-D-glutamate (γpDglu) monomers would exhibit a more flexible random coil conformation. The resulting macromers exhibited narrow molecular weight distributions (PDI = 1.15) and were grafted with ethylene glycol groups using a highly efficient "click" azide/alkyne cycloaddition reaction with average grafting efficiency of 97% for PPLG and 85% for PPDLG. The polypeptide secondary structure, characterized via circular dichroism spectroscopy, FTIR spectroscopy, and dynamic light scattering, is indeed dependent upon monomer chirality: PPLG exhibits an α-helix conformation while PPDLG adopts a random coil conformation. Hydrogel networks produced by cross-linking either helical or random coil polypeptides with poly(ethylene glycol) (PEG) were analyzed for amount of swelling, gelation efficiency, and permeability to a model protein. In addition, the elastic modulus of helical and coil polypeptide gels was determined by AFM indentation in fluid. Importantly, we found that helical and coil polypeptide gels exhibited similar swelling and permeability but different stiffnesses, which correspond to predictions from the theory of semi-flexible chains.

Temperature Dependence of the Amide I Frequency as a Probe of Solvent Accessibility of the Protein Backbone

Infrared (IR) spectroscopy of proteins often focuses on the relationship between the amide I band and polypeptide secondary structure; IR spectra has been used to probe backbone conformation on a wide range of samples (solution, films, gels, and solids), at a broad range of time scales (from ns to days), and as a function of a variety of perturbations (solvent, ionic strength, presence of lipid membrane). Often ignored is the solvent dependence of the amide I mode. Solvent-backbone hydrogen bonding can have a large effect on the observed amide I frequency (1). In this work, we demonstrate that the temperature dependence of amide I bands can be used to determine the solvent exposure of the peptide backbone. We have compared the IR spectra as a function of temperature in a number of different protein systems, including small, alanine-based peptides that form alpha-helices in solution; short peptides that aggregate to form fibrous, beta-sheet rich fibrous structures; short, dynamic peptides lacking regular secondary structure; membrane-embedded peptides; and globular proteins. When backbone groups are buried from solvent, the amide I band frequencies are independent of temperature (in the range of 5°C to 75°C). By contrast, backbone groups exposed to (and hydrogen-bonded with) solvent water show a temperature dependence similar to that observed in solvated model compounds (2). When this approach is combined with specific isotope-labeling (3), site-specific information about solvent accessibility can be obtained from the variable-temperature IR spectra. (1) A. Starzyk, W. Barber-Armstrong, M. Sridharan and S. M. Decatur, Biochemistry, 2005, 44, 369. (2) K. E. Amunson and J. Kubelka J. Phys. Chem. B, 2007, 111, 9993. (3) S. M. Decatur, Acc. Chem. Res., 2006, 39, 169.