Two Dimensional Oblique Molecular Packing within a Model Peptide Ribbon Aggregate

Insights into the Hierarchical Assembly of a Chemically Diverse Peptide Hydrogel Derived from Human Semenogelin I

A peptide corresponding to a 13-residue segment of the human protein semenogelin I has been shown to generate a hydrogel consisting of amyloid-like fibrils. The relative chemical diversity (compared to synthetic de novo sequences) with 11 distinct amino acids makes this peptide (P0) an ideal candidate for investigating the role of individual residues in gelation. Herein, the N-terminal residues have been sequentially removed to furnish a series of truncated peptides, P1-P10, ranging from 12 to 3 residues in length. FTIR spectroscopy investigations reveal that P0-P6 forms a β-sheet secondary structure while shorter sequences do not self-assemble. Site-specific isotope labeling of the amide backbone of P0-P2 with the IR-sensitive vibrational probe 13C═O yields FTIR spectra indicative of the initial formation of a kinetic product that slowly transforms into a structurally different thermodynamic product. The effects of the isotopic labels on the IR spectra facilitate the assignment of parallel and antiparallel structures, which are sometimes coexistent. Additional IR studies of three PheCN-labeled P0 sequences are consistent with an H-bonded β-sheet amide core, spanning the 7 central residues. The macromolecular assembly of peptides that form β-sheets was assessed by cryo-TEM, SAXS/WAXS, and rheology. Cryo-TEM images of peptides P1-P6 display μm-long nanofibrils. Peptides P0-P3 generate homogeneous hydrogels composed of colloidally stable nanofibrils, and P4-P6 undergo phase separation due to the accumulation of attractive interfibrillar interactions. Three amino acid residues, Ser39, Phe40, and Gln43, were identified to be of particular interest in the truncated peptide series as the removal of any one of them, as the sequence shortens, leads to a major change in material properties.

Measuring mutual diffusion coefficients in aqueous binary mixtures with unidimensional drying cells

Chemical diffusion is a mass transport process caused by thermally generated motions of species. In a binary mixture, the diffusion of one species in one direction involves the diffusion of another species in the opposite direction, which corresponds to a single mutual diffusion coefficient. Here, we report a simple and general method to measure such coefficients in binary liquid mixtures, using the PNIPAM/water system as a study case. Experimentally, we show how a simple unidirectional drying cell coupled with a spatially-resolved characterization method such as Raman microscopy can yield concentration gradients developing in between two boundaries of known and constant chemical potential. Acquiring such gradients over time leads to a time-set that is shown to collapse to a single master curve using a change of variable. Such a scaling law offers a self-checking frame for solving analytically the diffusion-advection equation. As a result, we show that a simple analytical formula relates the measured concentration gradient with the concentration-dependent mutual diffusion coefficient. In the PNIPAM/water system, the mutual diffusion coefficient sharply decreases at low water content. Our work thus highlights the importance of considering the concentration-dependence of the mutual diffusion coefficient in complex aqueous solutions and provides a method to measure it.

Peptide-based assembled nanostructures that can direct cellular responses

Natural originated materials have been well-studied over the past several decades owing to their higher biocompatibility compared to the traditional polymers. Peptides, consisting of amino acids, are among the most popular programable building blocks, which is becoming a growing interest in nanobiotechnology. Structures assembled using those biomimetic peptides allow the exploration of chemical sequences beyond those been routinely used in biology. In this Review, we discussed the most recent experimental discoveries on the peptide-based assembled nanostructures and their potential application at the cellular level such as drug delivery. In particular, we explored the fundamental principles of peptide self-assembly and the most recent development in improving their interactions with biological systems. We believe that as the fundamental knowledge of the peptide assemblies evolves, the more sophisticated and versatile nanostructures can be built, with promising biomedical applications.

Amyloid β 42 fibril structure based on small-angle scattering

Amyloid fibrils are associated with a number of neurodegenerative diseases, including fibrils of amyloid β42 peptide (Aβ42) in Alzheimer's disease. These fibrils are a source of toxicity to neuronal cells through surface-catalyzed generation of toxic oligomers. Detailed knowledge of the fibril structure may thus facilitate therapeutic development. We use small-angle scattering to provide information on the fibril cross-section dimension and shape for Aβ42 fibrils prepared in aqueous phosphate buffer at pH = 7.4 and pH 8.0 under quiescent conditions at 37 °C from pure recombinant Aβ42 peptide. Fitting the data using a continuum model reveals an elliptical cross-section and a peptide mass-per-unit length compatible with two filaments of two monomers, four monomers per plane. To provide a more detailed atomistic model, the data were fitted using as a starting state a high-resolution structure of the two-monomer arrangement in filaments from solid-state NMR (Protein Data Bank ID 5kk3). First, a twofold symmetric model including residues 11 to 42 of two monomers in the filament was optimized in terms of twist angle and local packing using Rosetta. A two-filament model was then built and optimized through fitting to the scattering data allowing the two N-termini in each filament to take different conformations, with the same conformation in each of the two filaments. This provides an atomistic model of the fibril with twofold rotation symmetry around the fibril axis. Intriguingly, no polydispersity as regards the number of filaments was observed in our system over separate samples, suggesting that the two-filament arrangement represents a free energy minimum for the Aβ42 fibril.

Slow Dissolution Kinetics of Model Peptide Fibrils

Understanding the kinetics of peptide self-assembly is important because of the involvement of peptide amyloid fibrils in several neurodegenerative diseases. In this paper, we have studied the dissolution kinetics of self-assembled model peptide fibrils after a dilution quench. Due to the low concentrations involved, the experimental method of choice was isothermal titration calorimetry (ITC). We show that the dissolution is a strikingly slow and reaction-limited process, that can be timescale separated from other rapid processes associated with dilution in the ITC experiment. We argue that the rate-limiting step of dissolution involves the breaking up of inter-peptide β–sheet hydrogen bonds, replacing them with peptide–water hydrogen bonds. Complementary pH experiments revealed that the self-assembly involves partial deprotonation of the peptide molecules.

Tube to ribbon transition in a self-assembling model peptide system

Peptides that self-assemble into β-sheet rich aggregates are known to form a large variety of supramolecular shapes, such as ribbons, tubes or sheets. However, the underlying thermodynamic driving forces for such different structures are still not fully understood, limiting their potential applications. In the A_nK peptide system (A = alanine, K = lysine), a structural transition from tubes to ribbons has been shown to occur upon an increase of the peptide length, n, from 6 to 8. In this work we analyze this transition by means of a simple thermodynamic model. We consider three energy contributions to the total free energy: an interfacial tension, a penalty for deviating from the optimal β-sheet twist angle, and a hydrogen bond deformation when the β-sheets adopt a specific self-assembled structure. Whilst the first two contributions merely provide similar constant energy offsets, the hydrogen bond deformations differ depending on the studied structure. Consequently, the tube structure is thermodynamically favored for shorter A_nK peptides, with a crossover at n≈ 13. This qualitative agreement of the model with the experimental observations shows, that we have achieved a good understanding of the underlying thermodynamic features within the self-assembling A_nK system.

Self-Assembly of Model Amphiphilic Peptides in Nonaqueous Solvents: Changing the Driving Force for Aggregation Does Not Change the Fibril Structure

Within the homologous series of amphiphilic peptides A_nK, both A₈K and A₁₀K self-assemble in water to form twisted ribbon fibrils with lengths around 100 nm. The structure of the fibrils can be described in terms of twisted β-sheets extending in the direction of the fibrils, laminated to give a constant cross section of 4 nm by 8 nm. The finite width of the twisted ribbons can be reasonably explained within a simple thermodynamic model, considering a free energy penalty for the stretching of hydrogen bonds along the twisted β-sheets and an interfacial free energy gain for the lamination of the hydrophobic β-sheets. In this study, we characterize the self-assembly behavior of these peptides in nonaqueous solutions as a route to probe the role of hydrophobic interaction in fibril stabilization. Both peptides, in methanol and N,N-dimethylformamide, were found to form fibrillar aggregates with the same β-sheet structure as in water but with slightly smaller cross-sectional sizes. However, the gel-like texture, the slow relaxation in dynamic light scattering experiments, and a correlation peak in the small-angle X-ray scattering pattern highlighted enhanced interfibril interactions in the nonaqueous solvents in the same concentration range. This could be ascribed to a higher effective volume of the aggregates because of enhanced fibril growth and length, as suggested by light scattering and cryogenic transmission electron microscopy analyses. These effects can be discussed considering how the solvent properties affect the different energetic contributions (hydrophobic, electrostatic, and hydrogen bonding) to fibril formation. In the analyzed case, the decreased hydrogen bonding propensity of the nonaqueous solvents makes the hydrogen bond formation along the fibril a key driving force for peptide assembly, whereas it represents a nonrelevant contribution in water.

Two Dimensional Oblique Molecular Packing within a Model Peptide Ribbon Aggregate

A10 K (A=alanine, K=lysine) model peptides self-assemble into ribbon-like β-sheet aggregates. Here, we report an X-ray diffraction investigation on a flow-aligned dispersion of these self-assembly structures. The two-dimensional wide-angle X-ray scattering pattern suggests that peptide pack in a two-dimensional oblique lattice, essentially identical to the crystalline packing of polyalanine, An (for n>4). One side of the oblique unit cell, corresponding to the anti-parallel β-sheet, is oriented along the ribbon's axis. Together with recently published small angle X-ray scattering data of the same system, this work thus yields a detailed description of the self-assembled ribbon aggregates, down to the molecular length scale. Notably, our results highlight the importance of the crystalline peptide packing within its self-assembly aggregates, which is often neglected.

Arrested dynamics in a model peptide hydrogel system

We report here on a peptide hydrogel system, which in contrast to most other such systems, is made up of relatively short fibrillar aggregates, discussing resemblance with colloidal rods. The synthetic model peptides A₈K and A₁₀K, where A denotes alanine and K lysine, self-assemble in aqueous solutions into ribbon-like aggregates having an average length 〈L〉 on the order of 100 nm and with a diameter d≈ 6 nm. The aggregates can be seen as weakly charged rigid rods and they undergo an isotropic to nematic phase transition at higher concentrations. Translational motion perpendicular to the rod axis gets strongly hindered when the concentration is increased above the overlap concentration. Similarly, the rotational motion is hindered, leading to very long stress relaxation times. The peptide self-assembly is driven by hydrophobic interactions and due to a net peptide charge the system is colloidally stable. However, at the same time short range, presumably hydrophobic, attractive interactions appear to affect the rheology of the system. Upon screening the long range electrostatic repulsion, with the addition of salt, the hydrophobic attraction becomes more dominant and we observe a transition from a repulsive glassy state to an attractive gel-state of the rod-like peptide aggregates.