Yurong Zhao

Tuning the Self-Assembly of Short Peptides via Sequence Variations

Peptide self-assembly is of direct relevance to protein science and bionanotechnology, but the underlying mechanism is still poorly understood. Here, we demonstrate the distinct roles of the noncovalent interactions and their impact on nanostructural templating using carefully designed hexapeptides, I2K2I2, I4K2, and KI4K. These simple variations in sequence led to drastic changes in final self-assembled structures. β-sheet hydrogen bonding was found to favor the formation of one-dimensional nanostructures, such as nanofibrils from I4K2 and nanotubes from KI4K, but the lack of evident β-sheet hydrogen bonding in the case of I2K2I2 led to no nanostructure formed. The lateral stacking and twisting of the β-sheets were well-linked to the hydrophobic and electrostatic interactions between amino acid side chains and their interplay. For I4K2, the electrostatic repulsion acted to reduce the hydrophobic attraction between β-sheets, leading to their limited lateral stacking and more twisting, and final fibrillar structures; in contrast, the repulsive force had little influence in the case of KI4K, resulting in wide ribbons that eventually developed into nanotubes. The fibrillar and tubular features were demonstrated by a combination of cryogenic transmission electron microscopy (cryo-TEM), negative-stain transmission electron microscopy (TEM), and small-angle neutron scattering (SANS). SANS also provided structural information at shorter scale lengths. All atom molecular dynamics (MD) simulations were used to suggest possible molecular arrangements within the β-sheets at the very early stage of self-assembly.

Solvent Controlled Structural Transition of KI4K Self-Assemblies: from Nanotubes to Nanofibrils

The structural modulation of peptide and protein assemblies under well-controlled conditions is of both fundamental and practical significance. In spite of extensive studies, it remains hugely challenging to tune the self-assembled nanostructures in a controllable manner because the self-assembly processes are dictated by various noncovalent interactions and their interplay. We report here how to manipulate the self-assembly of a designed, symmetric amphiphilic peptide (KI4K) via the solvent-controlled structural transition. Structural transition processes were carefully followed by the combination of transmission electronic microscopy (TEM), atomic force microscopy (AFM), circular dichroism (CD), Fourier transform infrared spectroscopy (FTIR), and small angle neutron scattering (SANS). The results show that the introduction of acetonitrile into water significantly affected the hydrophobic interactions among hydrophobic side chains while imposing little impact on the β-sheet hydrogen bonding between peptide backbones. A structural transition occurred from nanotubes to helical/twisted ribbons and then to thin fibrils with the addition of acetonitrile due to the reduced hydrophobic interactions and the consequent weakening of the lateral stacking between KI4K β-sheets. The increased intermolecular electrostatic repulsions among lysine side chain amino groups had little effect on the lateral stacking of KI4K β-sheets due to the molecular symmetry. Complementary molecular dynamic (MD) simulations also indicated the solvation of acetonitrile molecules into the hydrophobic domains weakening the coherence between the neighboring sheets.

Construction of Supramolecular Self‐Assembled Microfibers with Fluorescent Properties through a Modified Ionic Self‐Assembly (ISA) Strategy

Highly ordered supramolecular microfibers were constructed through a simple ionic self-assembly strategy from complexes of the N-tetradecyl-N-methylpyrrolidinium bromide (C(14)MPB) surface-active ionic liquid and the small methyl orange (MO) dye molecule, with the aid of patent blue VF sodium salt. By using scanning electron microscopy and polarized optical microscopy, the width of these self-assembled microfibers is observed to be about 1 to 5 μm and their length is from tens of micrometers to almost a millimeter. The (1)H NMR spectra of the microfibers indicates that the supramolecular complexes are composed of C(14)MPB and MO in equal molar ratio. The electrostatic, hydrophobic, and π-π stacking interactions are regarded as the main driving forces for the formation of microfibers. Furthermore, through characterization by using confocal fluorescence microscopy, the microfibers were observed to show strong fluorescent properties and may find potential applications in many fields.

Left or Right: How Does Amino Acid Chirality Affect the Handedness of Nanostructures Self-Assembled from Short Amphiphilic Peptides?

Peptide and protein fibrils have attracted an enormous amount of interests due to their relevance to many neurodegenerative diseases and their potential applications in nanotechnology. Although twisted fibrils are regarded as the key intermediate structures of thick fibrils or bundles of fibrils, the factors determining their twisting tendency and their handedness development from the molecular to the supramolecular level are still poorly understood. In this study, we have designed three pairs of enantiomeric short amphiphilic peptides: LI3LK and DI3DK, LI3DK and DI3LK, and LaI3LK and DaI3DK, and investigated the chirality of their self-assembled nanofibrils through the combined use of atomic force microscopy (AFM), circular dichroism (CD) spectroscopy, scanning electron microscopy (SEM), and molecular dynamic (MD) simulations. The results indicated that the twisted handedness of the supramolecular nanofibrils was dictated by the chirality of the hydrophilic Lys head at the C-terminal, while their characteristic CD signals were determined by the chirality of hydrophobic Ile residues. MD simulations delineated the handedness development from molecular chirality to supramolecular handedness by showing that the β-sheets formed by LI3LK, LaI3LK, and DI3LK exhibited a propensity to twist in a left-handed direction, while the ones of DI3DK, DaI3DK, and LI3DK in a right-handed twisting orientation.

Molecular Origin of the Self-Assembled Morphological Difference Caused by Varying the Order of Charged Residues in Short Peptides

In order to understand how microscopic molecular interactions between short peptides determine their mesoscopic self-assembled morphology, we studied the microscopic assembled structures of the short peptides I4K2 and KI4K, which have the same amino acid composition but different sequences, by using all-atom replica exchange molecular dynamics simulation. We found that, at room temperature, the difference in amino acid sequence does not apparently alter their strong propensity of forming β-sheets but does strongly affect their assembled stable structures and their appearance probabilities. These differences result from the competition between the electrostatic and hydrophobic interactions among the side chains of the molecules, which are linked up by hydrogen bonds formed between neighboring peptide backbones. Our simulation results not only reveal the molecular origin of the self-assembled morphological difference between I4K2 and KI4K but also demonstrate in general the subtle balance between electrostatic, hydrophobic, and hydrogen bonding interactions in short-peptide self-assembly.

Peptide-templated synthesis of branched MnO2 nanowires with improved electrochemical performances

Although many nanomaterials have been prepared in vitro by mimicking biomineralization, the biomimetic synthesis of hybrids with both well-ordered nanostructures and specific functions is still in its infancy. A short designed peptide amphiphile I3K can form uniform and stable nanofibers in aqueous solution, with a surface enriched in cationic lysine residue. In the present study, we have demonstrated that the peptide nanofibers could direct the synthesis of MnO2 nanowires under mild conditions. By varying the concentration of manganese precursors (KMnO4 and Mn(NO3)2), uniform branched MnO2/peptide hybrid nanowires with high porosity and a large specific surface area were obtained. The well-defined MnO2 hybrid nanowires showed significantly improved electrochemical supercapacitive properties relative to compact MnO2 nanowires and urchin-like MnO2 spheres. Their specific capacitance could attain a higher value of 421 F g−1 and retained about 93% of the initial capacitance after 2500 cycles at a scan rate of 5 mV s−1, and remained little changed during the process of progressively varying the current density. Furthermore, the electrode prepared from the uniform MnO2 hybrid nanowires showed an excellent reversibility and a reasonably high-rate capability during the charge/discharge process. Such a study provides a new methodology to prepare functional MnO2 nanostructures under mild conditions that can be used in electrochemical energy storage.

Tuning One-Dimensional Nanostructures of Bola-Like Peptide Amphiphiles by Varying the Hydrophilic Amino Acids.

By combining experimental measurements and computer simulations, we here show that for the bola-like peptide amphiphiles XI4 X, where X=K, R, and H, the hydrophilic amino acid substitutions have little effect on the β-sheet hydrogen-bonding between peptide backbones. Whereas all of the peptides self-assemble into one dimensional (1D) nanostructures with completely different morphologies, that is, nanotubes and helical nanoribbons for KI4 K, flat and multilayered nanoribbons for HI4 H, and twisted and bilayered nanoribbons for RI4 R. These different 1D morphologies can be explained by the distinct stacking degrees and modes of the three peptide β-sheets along the x-direction (width) and the z-direction (height), which microscopically originate from the hydrogen-bonding ability of the sheets to solvent molecules and the pairing of hydrophilic amino acid side chains between β-sheet monolayers through stacking interactions and hydrogen bonding. These different 1D nanostructures have distinct surface chemistry and functions, with great potential in various applications exploiting the respective properties of these hydrophilic amino acids.

Intrinsic defect formation in peptide self-assembly

In contrast to extensively studied defects in traditional materials, we report here a systematic investigation of the formation mechanism of intrinsic defects in self-assembled peptide nanostructures. The Monte Carlo simulations with our simplified dynamic hierarchical model revealed that the symmetry breaking of layer bending mode at the two ends during morphological transformation is responsible for intrinsic defect formation, whose microscopic origin is the mismatch between layer stacking along the side-chain direction and layer growth along the hydrogen bond direction. Moreover, defect formation does not affect the chirality of the self-assembled structure, which is determined by the initial steps of the peptide self-assembly process.

Influence of Conventional Surfactants on the Self-Assembly of a Bola Type Amphiphilic Peptide

Structural and morphological regulation is a distinctly important topic in peptide self-assembly, and is also regarded as the fundamental point in peptide-based biomaterials development. In this paper, we showed that adding anionic surfactant SDS to a bola amphiphilic peptide KI4K could result in the reconstruction of β-sheet secondary structure besides the changes in self-assembly morphologies from nanotubes to helical ribbons, nanofibers, or straight nanotapes according to the negatively stained transmission electron microscopy, atomic force microscopy, circular dichroism spectroscopy, and Fourier transform infrared spectroscopy results. The inducing effect of SDS was observed at both above and below its CMC but with different transformation rates. Through comparison to other surfactants, including CTAB, C12EO4, and AOT, we proposed that the transitions of KI4K self-assemblies induced by anionic surfactants could be mainly attributed to the effect of hydrophobic interaction and electrostatic attraction between surfactants and peptide molecules. Rheological property measurement and dye adsorption experiments were also carried out to evaluate the properties of hydrogels formed by the peptide/surfactant hybrids. The samples formed self-supporting hydrogels at proper SDS or AOT concentrations, and the charges of hydrogel could be regulated by peptide to surfactant ratio.

Anisotropic formation mechanism and nanomechanics for the self-assembly process of cross-β peptides

Nanostructures self-assembled by cross-β peptides with ordered structures and advantageous mechanical properties have many potential applications in biomaterials and nanotechnologies. Quantifying the intra- and inter-molecular driving forces for peptide self-assembly at the atomistic level is essential for understanding the formation mechanism and nanomechanics of various morphologies of self-assembled peptides. We investigate the thermodynamics of the intra- and inter-sheet structure formations in the self-assembly process of cross-β peptide KIIIIK by means of steered molecular dynamics simulation combined with umbrella sampling. It is found that the mechanical properties of the intra- and inter-sheet structures are highly anisotropic with their intermolecular bond stiffness at the temperature of 300 K being 5.58 N/m and 0.32 N/m, respectively. This mechanical anisotropy comes from the fact that the intra-sheet structure is stabilized by enthalpy but the inter-sheet structure is stabilized by entropy. Moreover, the formation process of KIIIIK intra-sheet structure is cooperatively driven by the van der Waals (VDW) interaction between the hydrophobic side chains and the electrostatic interaction between the hydrophilic backbones, but that of the inter-sheet structure is primarily driven by the VDW interaction between the hydrophobic side chains. Although only peptide KIIIIK is studied, the qualitative conclusions on the formation mechanism should also apply to other cross-β peptides.