Beware of Cocktails: Chain-Length Bidispersity Triggers Explosive Self-Assembly of Poly-L-Glutamic Acid β2-Fibrils

Bulk Biopolyelectrolyte Complexes from Homopolypeptides: Solid "Salt Bridges"

Salt bridges, pairings between oppositely charged amino acids, are dispersed throughout proteins to assist folding and interactions. Biopolyelectrolyte complexes (BioPECs) were made between the homopolypeptides poly-l-arginine (PLR) and poly-l-lysine (PLK) with sodium triphosphate (STPP), as well as from polypeptide-only combinations. Viscoelastic measurements on these high salt bridge density materials showed many were solid, even glassy, in nature. Although the polypeptide-phosphate complexes had similar moduli at room temperature, the PLR-STPP complex displayed an unusual melting event above 70 °C not seen in PLK-STPP. This event was supported with differential scanning calorimetry. Infrared spectroscopy showed the PLK-STPP system contained β-sheets, while PLR-STPP did not. Stoichiometric, macroscopic BioPECs of PLR and PLK with poly-l-aspartic acid (PLD) and poly-l-glutamic acid (PLE) were made. PLR-PLD was found to undergo a melting event similar to that in PLR-STPP. ATR-FTIR studies showed that BioPECs made with PLD do not contain β-sheets, while those composed of PLE do. This work illustrates an expanded palette of unique properties from these biomaterials, such as strong viscoelastic differences between PECs containing PLE and PLD, even though they differ by only one carbon on the side chain.

Folding and self-assembly of short intrinsically disordered peptides and protein regions

Proteins and peptide fragments are highly relevant building blocks in self-assembly for nanostructures with plenty of applications. Intrinsically disordered proteins (IDPs) and protein regions (IDRs) are defined by the absence of a well-defined secondary structure, yet IDPs/IDRs show a significant biological activity. Experimental techniques and computational modelling procedures for the characterization of IDPs/IDRs are discussed. Directed self-assembly of IDPs/IDRs allows reaching a large variety of nanostructures. Hybrid materials based on the derivatives of IDPs/IDRs show a promising performance as alternative biocides and nanodrugs. Cell mimicking, in vivo compartmentalization, and bone regeneration are demonstrated for IDPs/IDRs in biotechnological applications. The exciting possibilities of IDPs/IDRs in nanotechnology with relevant biological applications are shown.

Reduction of a disulfide-constrained oligo-glutamate peptide triggers self-assembly of β2-type amyloid fibrils with the chiroptical properties determined by supramolecular chirality

Disulfide bonds prevent aggregation of globular proteins by stabilizing the native state. However, a disulfide bond within a disordered state may accelerate amyloidogenic nucleation by navigating fluctuating polypeptide chains towards an orderly assembly of β-sheets. Here, the self-assembly behavior of Glu-Cys-(Glu)₄-Cys-Glu peptide (E₆C₂), in which an intrachain disulfide bond is engineered into an amyloidogenic homopolypeptide motif, is investigated. To this end, the Thioflavin T (ThT) fluorescence kinetic assay is combined with infrared spectroscopy, circular dichroism (CD), atomic force microscopy (AFM) and Raman scattering measurements. Regardless of whether the disulfide bond is intact or reduced, E₆C₂ monomers remain disordered within a broad range of pH. On the other hand, only reduced E₆C₂ self-assembles into amyloid fibrils with the unique infrared traits indicative of three-center hydrogen bonds involving main-chain carbonyl as a bifurcating acceptor and main-chain NH and side-chain -COOH groups as hydrogen donors: the bonding pattern observed in so-called β₂-fibrils. AFM analysis of β₂-E₆C₂ reveals tightly packed rectangular superstructures whose presence coincides with strong chiroptical properties. Our findings suggest that formation of chiral amyloid superstructures may be a generic process accessible to various substrates, and that the fully extended conformation of a poly-Glu chain is a condition sine qua non for self-assembly of β₂-fibrils.

pH-Induced Changes in Polypeptide Conformation: Force-Field Comparison with Experimental Validation

Microsecond-long all-atom molecular dynamics (MD) simulations, circular dichroism, laser Doppler velocimetry, and dynamic light-scattering techniques have been used to investigate pH-induced changes in the secondary structure, charge, and conformation of poly l-lysine (PLL) and poly l-glutamic acid (PGA). The employed combination of the experimental methods reveals for both PLL and PGA a narrow pH range at which they are charged enough to form stable colloidal suspensions, maintaining their α-helix content above 60%; an elevated charge state of the peptides required for colloidal stability promotes the peptide solvation as a random coil. To obtain a more microscopic view on the conformations and to verify the modeling performance, peptide secondary structure and conformations rising in MD simulations are also examined using three different force fields, i.e., OPLS-AA, CHARMM27, and AMBER99SB*-ILDNP. Ramachandran plots reveal that in the examined setup the α-helix content is systematically overestimated in CHARMM27, while OPLS-AA overestimates the β-sheet fraction at lower ionization degrees. At high ionization degrees, the OPLS-AA force-field-predicted secondary structure fractions match the experimentally measured distribution most closely. However, the pH-induced changes in PLL and PGA secondary structure are reasonably captured only by the AMBER99SB*-ILDNP force field, with the exception of the fully charged PGA in which the α-helix content is overestimated. The comparison to simulations results shows that the examined force fields involve significant deviations in their predictions for charged homopolypeptides. The detailed mapping of secondary structure dependency on pH for the polypeptides, especially finding the stable colloidal α-helical regime for both examined peptides, has significant potential for practical applications of the charged homopolypeptides. The findings raise attention especially to the pH fine tuning as an underappreciated control factor in surface modification and self-assembly.

Aggregation rate of amyloid beta peptide is controlled by beta-content in monomeric state

Understanding the key factors that govern the rate of protein aggregation is of immense interest since protein aggregation is associated with a number of neurodegenerative diseases. Previous experimental and theoretical studies have revealed that the hydrophobicity, charge, and population of the fibril-prone monomeric state control the fibril formation rate. Because the fibril structures consist of cross beta sheets, it is widely believed that those sequences that have a high beta content (β) in the monomeric state should have high aggregation rates as the monomer can serve as a template for fibril growth. However, this important fact has never been explicitly proven, motivating us to carry out this study. Using replica exchange molecular dynamics simulation with implicit water, we have computed β of 19 mutations of amyloid beta peptide of 42 residues (Aβ42) for which the aggregation rate κ has been measured experimentally. We have found that κ depends on β in such a way that the higher the propensity to aggregation, the higher the beta content in the monomeric state. Thus, we have solved a long-standing problem of the dependence of fibril formation time of the β-structure on a quantitative level.

Neglected Hydrophobicity of Dimethanediyl Group in Peptide Self-Assembly: A Hint from Amyloid-like Peptide GNNQQNY and Its Derivatives

Besides typical hydrophobic amino acids providing hydrophobic interactions, glutamine as a hydrophilic amino acid has also been known to be an important element in many self-assembling peptides, but it is still not clear how this particular amino acid contributes to the self-assembling process. We supposed that the dimethanediyl group in the side chain of glutamine could provide hydrophobic interaction for peptide self-assembly. To prove this hypothesis, we used the GNNQQNY peptide and its derivatives as examples to show the importance of the dimethanediyl group for peptide self-assembly. We found a very close relationship between the number of dimethanediyl groups, the strength of hydrophobic interaction, and the self-assembling ability of the peptides, indicating the hydrophobicity of the dimethanediyl group and its important role for self-assembly. This new finding might be instructive for clarifying the self-assembling mechanism of many natural peptides, as well as for developing novel self-assembling peptide nanomaterials.

Secondary structures in synthetic polypeptides from N-carboxyanhydrides: design, modulation, association, and material applications

This article highlights the conformation-specific properties and functions of synthetic polypeptides derived from N-carboxyanhydrides.

Conformations and molecular interactions of poly-γ-glutamic acid as a soluble microbial product in aqueous solutions

Soluble microbial products (SMPs) are of significant concern in the natural environment and in engineered systems. In this work, poly-γ-glutamic acid (γ-PGA), which is predominantly produced by Bacillus sp., was investigated in terms of pH-induced conformational changes and molecular interactions in aqueous solutions; accordingly, its sedimentation coefficient distribution and viscosity were also elucidated. Experimental results indicate that pH has a significant impact on the structure and molecular interactions of γ-PGA. The conformation of the γ-PGA acid form (γ-PGA-H) is rod-like while that of the γ-PGA sodium form (γ-PGA-Na) is sphere-like. The transformation from α-helix to random coil in the γ-PGA secondary structure is primarily responsible for this shape variation. The intramolecular hydrogen bonds in the γ-PGA-H structure decrease and intramolecular electrostatic repulsion increases as pH increases; however, the sedimentation coefficient distributions of γ-PGA are dependent on intermolecular interactions rather than intramolecular interactions. Concentration has a more substantial effect on intermolecular electrostatic repulsion and chain entanglement at higher pH values. Consequently, the sedimentation coefficient distributions of γ-PGA shift significantly at pH 8.9 from 0.1 to 1.0 g/L, and the viscosity of γ-PGA (5% w/v) significantly increases as pH increases from 2.3 to 6.0.

Effects of terminal capping on the fibrillation of short (L-Glu)n peptides

Several homopolypeptides including poly-l-glutamic acid (PLGA) form amyloid-like fibrils under favorable physicochemical conditions. We have shown recently that even short uncapped (Glu)_n peptides (for n>3) form fibrillar β-aggregates which cross-seed with amyloid fibrils obtained from high molecular weight fractions of PLGA. Here we investigate effects of N-terminal acetylation and C-terminal amidation on the amyloidogenic tendencies of (Glu)_n peptides containing 3, 4, and 5 residues. Our results based primarily on time-lapse FT-IR spectroscopy and AFM microscopy indicate that selective modifications of C-termini (and, to a lesser degree, of N-termini) decrease capacity of tetra- and pentapeptides to form fibrils. On the other hand, peptides modified at both ends appear to form fibrils as fast as unmodified analogues. In fact, the double terminal modification enables fibrillation of (Glu)₃ which is not fibrillogenic in the unmodified state. The AFM data suggests that the double capping results in the aggregates becoming more tape-like or acquiring noticeable tendencies to bend. According to seeding and cross-seeding experiments, there is a high degree of promiscuity between modified and unmodified peptides. Possible mechanisms explaining how amyloidogenic propensities of (Glu)_n peptides are affected by terminal modifications have been discussed.