Random Coil Peptide Research Articles

Monomer Composition as a Mechanism to Control the Self-Assembly of Diblock Oligomeric Peptide-Polymer Amphiphiles.

Diblock oligomeric peptide-polymer amphiphiles (PPAs) are biohybrid materials that offer versatile functionality by integrating the sequence-dependent properties of peptides with the synthetic versatility of polymers. Despite their potential as biocompatible materials, the rational design of PPAs for assembly into multichain nanoparticles remains challenging due to the complex intra- and intermolecular interactions emanating from the polymer and peptide segments. To systematically explore the impact of monomer composition on nanoparticle assembly, PPAs were synthesized with a random coil peptide (XTEN2) and oligomeric alkyl acrylates with different side chains: ethyl, tert-butyl, n-butyl, and cyclohexyl. Experimental characterization using electron and atomic force microscopies demonstrated that the tail hydrophobicity impacted accessible morphologies. Moreover, the characterization of different assembly protocols (i.e., bath sonication and thermal annealing) revealed that certain tail compositions provide access to kinetically trapped assemblies. All-atom molecular dynamics simulations of micelle formation unveiled key interactions and differences in core hydration, dictating the PPA assembly behavior. These findings highlight the complexity of PPA assembly dynamics and serve as valuable benchmarks to guide the design of PPAs for a variety of applications, including catalysis, mineralization, targeted sequestration, antimicrobial activity, and cargo transportation.

Helical peptide structure improves conductivity and stability of solid electrolytes.

Ion transport is essential to energy storage, cellular signalling and desalination. Polymers have been explored for decades as solid-state electrolytes by either adding salt to polar polymers or tethering ions to the backbone to create less flammable and more robust systems. New design paradigms are needed to advance the performance of solid polymer electrolytes beyond conventional systems. Here the role of a helical secondary structure is shown to greatly enhance the conductivity of solvent-free polymer electrolytes using cationic polypeptides with a mobile anion. Longer helices lead to higher conductivity, and random coil peptides show substantially lower conductivity. The macrodipole of the helix increases with peptide length, leading to larger dielectric constants. The hydrogen bonding of the helix also imparts thermal and electrochemical stability, while allowing for facile dissolution back to monomer in acid. Peptide polymer electrolytes present a promising platform for the design of next-generation ion-transporting materials.

Including the Ensemble of Unstructured Conformations in the Analysis of Protein's Native State by High-Pressure NMR Spectroscopy.

The analysis of pressure induced changes in the chemical shift of proteins allows statements on structural fluctuations proteins exhibit at ambient pressure. The inherent issue of separating general pressure effects from structural related effects on the pressure dependence of chemical shifts has so far been addressed by considering the characteristics of random coil peptides on increasing pressure. In this work, chemically and pressure denatured states of the cold shock protein B from Bacillus subtilis (BsCspB) have been assigned in 2D 1H-15N HSQC NMR spectra and their dependence on increasing hydrostatic pressure has been evaluated. The pressure denatured polypeptide chain has been used to separate general from structural related effects on 1H and 15N chemical shifts of native BsCspB and the implications on the interpretation of pressure induced changes in the chemical shift regarding the structure of BsCspB are discussed. It has been found that the ensemble of unstructured conformations of BsCspB shows different responses to increasing pressure than random coil peptides do. Thus, the approach used for considering the general effects that arise when hydrostatic pressure increases changes the structural conclusions that are drawn from high pressure NMR spectroscopic experiments that rely on the analysis of chemical shifts.

Analyse des Nativen Zustands von Proteinen durch Hochdruck NMR‐Spektroskopie unter Berücksichtigung des Ensembles Unstrukturierter Konformationen

AbstractDie Analyse druckabhängiger Änderungen der chemischen Verschiebung von Proteinen erlaubt es, Aussagen über strukturelle Fluktuationen zu machen, die diese bereits bei Umgebungsdruck aufweisen. Das Problem, allgemeine Effekte, die mit einer Erhöhung des hydrostatischen Drucks einhergehen, von strukturell bedingten Effekten auf die chemische Verschiebung zu trennen, wurde bisher durch das Einbeziehen der Eigenschaften unstrukturierter Modellpeptide angegangen. In dieser Arbeit wurden chemische Verschiebungen in 2D 1H‐15N‐HSQC Spektren von chemisch als auch druckdenaturierten Zuständen des Kälteschockproteins B aus Bacillus Subtilis (BsCspB) zugeordnet und ihre Abhängigkeit von Änderungen des hydrostatischen Drucks ausgewertet. Die durch hydrostatischen Druck denaturierte Polypeptidkette wurde verwendet, um allgemeine Effekte von strukturbedingten Effekten auf 1H und 15N chemische Verschiebungen zu trennen. Daraus resultierende Interpretationen der druckabhängigen Änderungen der chemischen Verschiebungen werden im strukturellen Kontext diskutiert. Es wurde festgestellt, dass das Ensemble unstrukturierter Konformationen von BsCspB anders auf eine Erhöhung des Drucks reagiert, als es unstrukturierte Modellpeptide tun. Daraus kann geschlussfolgert werden, dass der Ansatz, mit dem man allgemeine Effekte, die durch eine Erhöhung des Drucks hervorgerufen werden, abschätzt, die strukturellen Rückschlüsse ändert, die anhand einer Analyse von chemischen Verschiebungen getroffen werden.

Early events during the aggregation of Aβ16-22-derived switch-peptides tracked using Protein Charge Transfer Spectra

BackgroundUnderstanding Aβ aggregation and inhibiting it at early stages is of utmost importance in treating Alzheimer's and other related amyloidogenic diseases. However, majority of the techniques to study Aβ aggregation mainly target the late stages; while those used to monitor early stages are either expensive, use extrinsic dyes, or do not provide information on molecular level interactions. Here, we investigate the early events of Aβ16-22(KLVFFAE) aggregation using Aβ16-22 derived switch-peptides (SwPs) through a novel label-free approach employing Protein Charge Transfer Spectra (ProCharTS). ResultsWhen pH is increased from 2 to 7.2, the Aβ-derived switch peptides undergo controlled self-assembly, where the initial random coil peptides convert into β-sheet. We leveraged the intrinsic absorbance/luminescence arising from ProCharTS among growing peptide oligomers to observe the aggregation kinetics in real-time. In comparison to monomer, the lysine and glutamate headgroups in the peptide oligomer are expected to come in proximity enhancing ProCharTS intensity due to photoinduced electron transfer. With a combination of Aβ-derived switch-peptides and ProCharTS, we obtained structural insights on the early stages of Aβ-derived SwP aggregation in four unique peptides. Increase in scatter corrected ProCharTS absorbance (250–500 nm) and luminescence (320–720 nm) along with decreased mean luminescence lifetime (2.3–0.8 ns) characterize the initial stages of aggregation monitored for 1–96 h depending on the peptide. We correlated the results with Circular Dichroism (CD), 8-anilino-1-naphthalenesulfonic acid (ANS) and Thioflavin T (ThT) measurements. SignificanceWe demonstrate ProCharTS as an intrinsic analytical probe with following advantages over other conventional methods to track aggregation: it is a label-free probe; it's intensity can be measured using a UV–Vis spectrophotometer; it is more sensitive in detecting the early molecular events in aggregation compared to ANS and ThT; and it can provide information on specific contacts made between charged headgroups of Lysine/Glutamate in the oligomer.

Persistence of Methionine Side Chain Mobility at Low Temperatures in a Nine-Residue Low Complexity Peptide, as Probed by 2 H Solid-State NMR.

Methionine side chains are flexible entities which play important roles in defining hydrophobic interfaces. We utilize deuterium static solid-state NMR to assess rotameric inter-conversions and other dynamic modes of the methionine in the context of a nine-residue random-coil peptide (RC9) with the low-complexity sequence GGKGMGFGL. The measurements in the temperature range of 313 to 161 K demonstrate that the rotameric interconversions in the hydrated solid powder state persist to temperatures below 200 K. Removal of solvation significantly reduces the rate of the rotameric motions. We employed 2 H NMR line shape analysis, longitudinal and rotation frame relaxation, and chemical exchange saturation transfer methods and found that the combination of multiple techniques creates a significantly more refined model in comparison with a single technique. Further, we compare the most essential features of the dynamics in RC9 to two different methionine-containing systems, characterized previously. Namely, the M35 of hydrated amyloid-β1-40 in the three-fold symmetric polymorph as well as Fluorenylmethyloxycarbonyl (FMOC)-methionine amino acid with the bulky hydrophobic group. The comparison suggests that the driving force for the enhanced methionine side chain mobility in RC9 is the thermodynamic factor stemming from distributions of rotameric populations, rather than the increase in the rate constant.

Intrinsic Fluorescence in Peptide Amphiphile Micelles with Protein-Inspired Phosphate Sensing.

Although peptide amphiphile micelles (PAMs) have been widely studied since they were developed in the late 1990s, to the author's knowledge, there have been no reports that PAMs intrinsically fluoresce without a fluorescent tag, according to the aggregation-induced emission (AIE) effect. This unexpected fluorescence behavior adds noteworthy value to both the peptide amphiphile and AIE communities. For PAMs, intrinsic fluorescence becomes another highly useful feature to add to this well-studied material platform that features precise synthetic control, tunable self-assembly, and straightforward functionalization, with clear potential applications in bioinspired materials for bioimaging and fluorescent sensing. For AIE, it is extremely rare and highly desirable for one platform to exhibit precise tunability on multiple length scales in aqeuous solutions, positioning PAMs as uniquely well-suited for systematic AIE mechanistic study and sequence-specific functionalization for bioinspired AIE applications. In this work, the author proposes that AIE occurs across intermolecular emissive pathways created by the closely packed peptide amide bonds in the micelle corona upon self-assembly, with maximum excitation and emission wavelengths of 355 and 430 nm, respectively. Of the three PAMs evaluated here, the PAM with tightly packed random coil peptide conformation and maximum peptide length had the largest quantum yield, indicating that tuning molecular design can further optimize the intrinsic emissive properties of PAMs. To probe the sensing capabilities of AIE PAMs, a PAM was designed to incorporate a protein-derived phosphate-binding sequence. It detected phosphate down to 1 ppm through AIE-enhanced second-order aggregation, demonstrating that AIE in PAMs leverages tunable biomimicry to perform protein-inspired sensing.

Mapping the Morphological Landscape of Oligomeric Di-block Peptide-Polymer Amphiphiles.

Peptide-polymer amphiphiles (PPAs) are tunable hybrid materials that achieve complex assembly landscapes by combining the sequence-dependent properties of peptides with the structural diversity of polymers. Despite their promise as biomimetic materials, determining how polymer and peptide properties simultaneously affect PPA self-assembly remains challenging. We herein present a systematic study of PPA structure-assembly relationships. PPAs containing oligo(ethyl acrylate) and random-coil peptides were used to determine the role of oligomer molecular weight, dispersity, peptide length, and charge density on self-assembly. We observed that PPAs predominantly formed spheres rather than anisotropic particles. Oligomer molecular weight and peptide hydrophilicity dictated morphology, while dispersity and peptide charge affected particle size. These key benchmarks will facilitate the rational design of PPAs that expand the scope of biomimetic functionality within assembled soft materials.

Liposome Deformation Induced by Random Coil and α-Helical Peptides

Liposome Deformation Induced by Random Coil and α-Helical Peptides

Investigations into the role of non-bond interaction on gelation mechanism of silk fibroin hydrogel.

Silk fibroin hydrogel not only has biocompatibility, but also has environmental response ability. It plays an important role in the development of material. The gelation mechanism of silk fibroin hydrogel is very important to textile and medicine fields. The molecular dynamics simulation was used to discuss the structure and non-bond interaction of silk fibroin hydrogel. The results show that the non-bond interactions between silk fibroin molecules and water molecules have certain influence on the formation of silk fibroin hydrogel. According to the hydrogen bond analysis, the hydrogen bonds are mainly formed between random coil peptide fragments at the two ends of silk fibroin molecules and residues 252-254 are the key residues. The electrostatic and polar solvation interactions between silk fibroin molecules plays a major role in cross-linking of the coil segments of two silk fibroin molecules.

Oligopeptide Helical Conformations Control Gold Nanoparticle Cross-Linking.

Peptide sequences functionalized with primary amines at the N- and C-terminus are able to induce the aggregation of gold nanoparticles in ethanol as a consequence of their folding into a helical conformation. Random coil peptides are unable to induce such an aggregation process. Aggregation can be monitored spectrophotometrically by following the shift of the surface plasmon resonance (SPR) band of the nanoparticles and is confirmed by transmission electron microscopy and dynamic light scattering analyses. Partial denaturation of the peptides results in diminished cross-linking ability. The helicity parameter θ222 /θ208 correlates fairly well with the shift of the SPR band to longer wavelengths, supporting the relationship between the amount of helical content of a peptide sequence and its ability to induce aggregation.

Random coil shifts of posttranslationally modified amino acids

Most eukaryotic proteins are modified during and/or after translation, regulating their structure, function and localisation. The role of posttranslational modifications (PTMs) in both normal cellular processes and in diseases is already well recognised and methods for detection of PTMs and generation of specifically modified proteins have developed rapidly over the last decade. However, structural consequences of PTMs and their specific effects on protein dynamics and function are not well understood. Furthermore, while random coil NMR chemical shifts of the 20 standard amino acids are available and widely used for residue assignment, dihedral angle predictions and identification of structural elements or propensity, they are not available for most posttranslationally modified amino acids. Here, we synthesised a set of random coil peptides containing common naturally occurring PTMs and determined their random coil NMR chemical shifts under standardised conditions. We highlight unique NMR signatures of posttranslationally modified residues and their effects on neighbouring residues. This comprehensive dataset complements established random coil shift datasets of the 20 standard amino acids and will facilitate identification and assignment of posttranslationally modified residues. The random coil shifts will also aid in determination of secondary structure elements and prediction of structural parameters of proteins and peptides containing PTMs.

M-Brucin, an antibacterial peptide against Staphylococcus epidermidis and Streptococcus pyogenes

Brucin, a specific antibacterial peptide against Strep. pyogenes was chemically synthesized and its amino acid sequence, NH2-His-Thr-Leu-Cys-Met-Asp-Gly-Gly-Ala-Thr-Tyr, was modified to improve the antibacterial activity. Only one from five-modified peptides with the sequence NH2-His-Thr-Leu-Cys-Met-Gly-Lys-Ala-Thr-Tyr possessed the antibacterial activity and it was designated as “M-Brucin”. Structural analysis of M-Brucin indicated that it was a linear with random coil peptide with a molecular mass of 1248.43 Da. It was a positive charge peptide (net charge = +1) with a pI value of 8.21 and hydrophobicity ratio of 40 %. The positive antimicrobial effect of M-Brucin was tested by agar dilution technique against 30 human-pathogenic bacteria and 1 fungus. Its inhibitory activity was tested against Staph. epidermidis and Streptococcus pyogenes DMST 17020 with IC50 values of 225 µM and 250 µM, respectively. Moreover, its inhibitory activity was identified as being as strong as penicillin G and chloramphenicol, with no toxicity to normal Vero cell at the same concentration tested. The results suggest that MB may be further developed as an alternative drug for the treatment of the disease caused by Strep.

Stereospecific assignment of the asparagine and glutamine sidechain amide protons in proteins from chemical shift analysis.

Side chain amide protons of asparagine and glutamine residues in random-coil peptides are characterized by large chemical shift differences and can be stereospecifically assigned on the basis of their chemical shift values only. The bimodal chemical shift distributions stored in the biological magnetic resonance data bank (BMRB) do not allow such an assignment. However, an analysis of the BMRB shows, that a substantial part of all stored stereospecific assignments is not correct. We show here that in most cases stereospecific assignment can also be done for folded proteins using an unbiased artificial chemical shift data base (UACSB). For a separation of the chemical shifts of the two amide resonance lines with differences ≥0.40ppm for asparagine and differences ≥0.42ppm for glutamine, the downfield shifted resonance lines can be assigned to Hδ21 and Hε21, respectively, at a confidence level >95%. A classifier derived from UASCB can also be used to correct the BMRB data. The program tool AssignmentChecker implemented in AUREMOL calculates the Bayesian probability for a given stereospecific assignment and automatically corrects the assignments for a given list of chemical shifts.

Effects and mechanisms of the secondary structure on the antimicrobial activity and specificity of antimicrobial peptides.

A 15-mer cationic α-helical antimicrobial peptide HPRP-A1 was used as the parent peptide to study the effects of peptide secondary structure on the biophysical properties and biological activities. Without changing the amino acid composition of HPRP-A1, we designed two α-helical peptides with either higher or lower helicity compared with the parent peptide, a β-sheet peptide and a random coiled peptide using de novo design approach. The secondary structures were confirmed by circular dichroism spectroscopy. The three α-helical peptides exhibited comparable antibacterial activities, but their hemolytic activity varied from extreme hemolysis to no hemolysis, which is correlated with their helicity. The β-sheet peptide shows poor antibacterial and strong hemolytic activities. More interestingly, the random coil peptide shows no antibacterial activity against Gram-negative bacteria, weak antibacterial activity against Gram-positive bacteria, and extremely weak hemolytic activity. Bacterial membrane permeabilization was also testified on peptides with different secondary structures. Tryptophan fluorescence experiment revealed that the peptide binding preference to the lipid vesicles for mimicking the prokaryotic or eukaryotic membranes was consistent with their biological activities. With the de novo design approach, we proved that it is important to maintain certain contents of amphipathic secondary structure for a desirable biological activity. We believe that the de novo design approach of relocation of the amino acids within a template sequence could be an effective approach in optimizing the specificity of an antimicrobial peptide.

Silica Mineralization by a Peptide Template Having a High Charge Relay Effect.

The influence of the charge relay effects of peptide organic templates on silica mineralization has been investigated. β-Sheet-type peptide showed higher catalytic activity towards the condensation of trimethylsilanol than random-coil peptides. The higher activity of the β-sheet peptide was attributed to an effective charge relay effect between the His and Glu residues of the β-sheet assembly. Furthermore, the silica mineralized on the VHVEVS peptide template formed a flat surface, which was affected by the peptide morphology. This result implied that the growth of the silica occurred at the surface of the peptide template in a manner very similar to that of the enzyme reaction. Thus, by using a specific structural design strategy, this process could be used for the preparation of specific silica particles.

Peptide–Column Interactions and Their Influence on Back Exchange Rates in Hydrogen/Deuterium Exchange-MS

Hydrogen/deuterium exchange (HDX) methods generate useful information on protein structure and dynamics, ideally at the individual residue level. Most MS-based HDX methods involve a rapid proteolytic digestion followed by LC/MS analysis, with exchange kinetics monitored at the peptide level. Localizing specific sites of HDX is usually restricted to a resolution the size of the host peptide because gas-phase processes can scramble deuterium throughout the peptide. Subtractive methods may improve resolution, where deuterium levels of overlapping and nested peptides are used in a subtractive manner to localize exchange to smaller segments. In this study, we explore the underlying assumption of the subtractive method, namely, that the measured back exchange kinetics of a given residue is independent of its host peptide. Using a series of deuterated peptides, we show that secondary structure can be partially retained under quenched conditions, and that interactions between peptides and reversed-phase LC columns may both accelerate and decelerate residue HDX, depending upon peptide sequence and length. Secondary structure is induced through column interactions in peptides with a solution-phase propensity for structure, which has the effect of slowing HDX rates relative to predicted random coil values. Conversely, column interactions can orient random-coil peptide conformers to accelerate HDX, the degree to which correlates with peptide charge in solution, and which can be reversed by using stronger ion pairing reagents. The dependency of these effects on sequence and length suggest that subtractive methods for improving structural resolution in HDX-MS will not offer a straightforward solution for increasing exchange site resolution.

PH-dependent helix folding dynamics of poly-glutamic acid

Poly-L-glutamic acid (PGA) is an ideal model system for investigating the transition between α-helical and random coil peptide conformations, since its secondary structure is highly sensitive not only to temperature, but also to pH. Laser pulse-induced temperature jumps were used to observe pH-dependent PGA helix–coil relaxation dynamics on the microsecond time scale. The relaxation was found to be non-exponential, particularly if only short helical segments are present before the temperature jump, indicating the multi-step nature of the process which involves helix nucleation and propagation. Helix–coil relaxation is slowest near the mid-point of the pH-induced helix–coil transition, in agreement with theoretical predictions.

Two-dimensional Self-assembly of Amphiphilic Peptide at the Solid/Water Interface toward a Facile Method for Metal Nanoparticle Alignment

Abstract An amphiphilic peptide that adopts a random-coil or β-sheet conformation depending on the pH of the dissolved aqueous solution forms a monolayered fiber array when a mica substrate is immersed in the random-coil solution. The random-coil peptide adsorbed on the substrate spontaneously transforms into a fibrous structure at the mica/water interface. Such specific self-assembly behavior at the solid/water interface is profitably utilized to construct a two-dimensional nanoarchitecture of gold nanoparticles.

On-Surface Assembly of Coiled-Coil Heterodimers

The coiled coil is a widespread protein motif responsible for directing the assembly of a wide range of protein complexes. To date, research has focused largely on the solution phase assembly of coiled-coil complexes. Here, we describe an investigation into coiled-coil heterodimer assembly where one of the peptides is immobilized directly onto a gold electrode. Immobilization is achieved by the introduction of a unique cysteine residue at the C terminus, allowing for covalent and orientated attachment to a thiol-reactive surface, here the gold electrode. We show an electrochemical impedance of the resulting self-assembled polypeptide monolayer around |Z| = 4 × 10(4) Ω cm(2) at 100 mHz with a minimum phase angle of -84°, consistent with the formation of a densely packed, insulating layer. The thickness of the peptide monolayer, as measured using ellipsometry, is around 3 nm, close to that expected for a self-assembled monolayer assembled from helical peptides. Crucially, we find that the efficiency of dimerization between a peptide in solution and its coiled-coil partner peptide immobilized on a surface is strongly dependent upon the density of the immobilized peptide layer, with dimer assembly being strongly suppressed by high-density peptide monolayers. We thus develop an approach for controlling the density of the immobilized peptide by diluting the monolayer with a thiolated, random-coil peptide to modulate dimerization efficiency and demonstrate electrochemical detection of highly specific, coiled-coil heterodimer on-surface assembly.