Predictive modeling of self assembly of chromonics materials

This study identifies mechanisms of self-assembly of a chromonic molecule with interesting self-assembly properties. Results from molecular dynamics (MD) studies used to understand the moieties of the molecule that affect the structure are consistent with experimental observations of these self-assembled structures. Coulombic forces, with significant contributions from π–π interactions drives the self-assembly of this class of materials; hydrogen bond energies are also significant.     

Why folates self-assemble: a simulation-based study

Folates (and other chromonics molecules) have been shown to self-assemble into ordered structures even at low concentrations. In this study, simulations are used to first replicate the self-assembly of folates and understand why folic acid does not assemble while folate ions do. Subsequently, these simulations replicate the change in structure and behaviour of the assembly with increasing concentration of folates, comparing them to experimental observations in earlier studies. The study then uses fictitious molecules and ions to understand which components of the folate ions drive, or otherwise affect, assembly of the folates and to abstract some guiding principles about structure of chromonics molecules and the impact on assembly. This study shows that while the aromatic rings drive stacking, the hydrophilic groups help solvate and hence control the order of the aromatic stacks, and the 1-ring-diacid moiety controls the orientation of the ions in their plane.     

Ricin antitoxins based on lyotropic mesophases containing galactose amphiphiles

Lyotropic mesophases of the inverse hexagonal or cubic type are nanostructured materials that result from the self-assembly of amphiphilic surfactant molecules in water. The extremely large area of the surfactant-water interface inherent within these structures makes them attractive media for sorbent or encapsulant systems. Here, we report on the development of a new class of polyvalent materials that are based on the incorporation of bioactive ligands within lyotropic mesophases. In particular, we have studied the potential for these materials to behave as polyvalent antitoxins by incorporating synthetic galactose amphiphiles, which mimic the natural cell surface ligand for the protein toxin ricin. The study demonstrates that cubic morphology lyotropic mesophases containing galactose amphiphiles exhibit high specificity ricin uptake, with favorably high dissociation constants and high capacities. We suggest that lyotropic mesophase polyvalent ligands are thus promising materials for the incorporation of a broad range of cell surface recognition moieties and hence may have wide applicability as materials capable of partaking in biological recognition processes.     

Simultaneous synthesis of temperature-tunable peptide and gold nanoparticle hybrid spheres

Hybrid spheres containing peptides and gold nanoparticles have been simultaneously synthesized in water using AG4 (NPSSLFRYLPSD) peptides that acted as a reducing agent to guide the nucleation and growth of gold nanoparticles and a precursor to form sphere-like structure by self-assembly where the size of hybrid spheres is precisely controlled by adjusting the operating temperature. The self-assembled peptide spheres remain stable even after selective removal of the gold nanoparticles by iodide etching. The amino acids containing the aromatic functional group in the peptide sequence significantly affect the construction of sphere structures. The surface of gold nanoparticles containing hybrid spheres has been functionalized using the thiol group linked to biomolecules. The ability to synthesize nanoparticle and self-assembled peptide structures with controlled size and composition in an environmental benign way will allow us to fabricate a new class of multifunctional organic-inorganic hybrid superstructures for various biomedical and electronic applications.     

Designed aromatic homo-dipeptides: formation of ordered nanostructures and potential nanotechnological applications

Molecular self-assembly offers new routes for the fabrication of novel materials at the nano-scale. Peptide-based nanostructures represent nano-objects of particular interest, as they are biocompatible, can be easily synthesized in large amounts, can be decorated with functional elements and can be used in various biological and non-biological applications. We had previously revealed the formation of highly ordered tubular structures by the diphenylalanine peptide, the core recognition motif of Alzheimer's beta-amyloid polypeptide, due to specific aromatic interactions. We further confirmed this model and demonstrated that a non-charged peptide analogue, Ac-Phe-Phe-NH2, self-assembled into similar tubular structures. We later explored other amine and carboxyl modified diphenylalanine peptide analogues and revealed that these dipeptides can form ordered tubular structures at the nanometric scale. Moreover, a very similar peptide, the diphenylglycine, self-assembled into ordered nano-spherical assemblies. Here we extend our research and explore the self-assembly of other homo-aromatic dipeptides in which their phenyl side-chains are modified with halogen atoms (di-para-fluoro-Phe, di-pentafluoro-Phe, di-para-iodo-Phe), additional phenyl groups (di-4-phenyl-Phe), or with nitro substitutions (di-para-nitro-Phe). We also probed the effect of the alteration of the phenyl groups with naphtyl groups (di-D-1-Nal and di-D-2-Nal). In all cases, well-ordered nanostructures were obtained and studied by scanning electron microscopy, transmission electron microscopy and vibrational spectroscopy. Taken together, the current work and previous ones define the homo-aromatic dipeptide as a central motif for the formation of ordered self-assembled tubular, spherical and two-dimensional structures at the nano-scale.     

自组装在多肽药物中的应用

自组装是指分子、纳米级结构材料等基本单元自发地组装成一个稳定而又紧密结构的过程。多肽可在各种非共价驱动力下自组装形成纳米纤维、纳米层状结构、胶束等不同的形貌。因多肽具有氨基酸序列明确、易于合成、便于设计等优势,多肽自组装技术成为了近年来的一个研究热点。有研究表明,对某些多肽类药物进行自组装设计或者使用自组装肽材料作为药物递送的载体,可以解决药物自身存在的半衰期短、水溶性差、生理屏障穿透率低等问题。本文重点介绍了自组装多肽的形成机制、自组装形貌、影响因素、自组装设计方法及其在生物医学领域的主要应用,为多肽的高效利用提供参考。     

Crystal structures of hydrophobin HFBII in the presence of detergent implicate the formation of fibrils and monolayer films

Hydrophobins are small, amphiphilic proteins secreted by filamentous fungi. Their functionality arises from a patch of hydrophobic residues on the protein surface. Spontaneous self-assembly of hydrophobins leads to the formation of an amphiphilic layer that remarkably reduces the surface tension of water. We have determined by x-ray diffraction two new crystal structures of Trichoderma reesei hydrophobin HFBII in the presence of a detergent. The monoclinic crystal structure (2.2A resolution, R = 22, R(free) = 28) is composed of layers of hydrophobin molecules where the hydrophobic surface areas of the molecules are aligned within the layer. Viewed perpendicular to the aligned hydrophobic surface areas, the molecules in the layer pack together to form six-membered rings, thus leaving small pores in the layer. Similar packing has been observed in the atomic force microscopy images of the self-assembled layers of class II hydrophobin, indicating that the crystal structure resembles that of natural hydrophobin film. The orthorhombic crystal structure (1.0 A resolution, R = 13, R(free) = 15) is composed of fiber-like arrays of protein molecules. Rodlet structures have been observed on amphiphilic layers formed by class I hydrophobins; fibrils of class II hydrophobins appear by vigorous shaking. We propose that the structure of the fibrils and/or rodlets is similar to that observed in the crystal structure.     

Probing the role of aromatic residues in the self-assembly of Aβ(16–22) in fluorinated alcohols and their aqueous mixtures

The Aβ(16–22) sequence KLVFFAE spans the hydrophobic core of the Aβ peptide and plays an important role in its self-assembly. Apart from forming amyloid fibrils, Aβ(16–22) can self-associate into highly ordered nanotubes and ribbon-like structures depending on the composition of solvent used for dissolution. The Aβ(16–22) sequence which has FF at the 19th and 20th positions would be a good model to investigate peptide self-assembly in the context of aromatic interactions. In this study, self-assembly of Aβ(16–22) and its aromatic analogs obtained by replacement of F19, F20 or both by Y or W was examined after dissolution in fluorinated alcohols and their aqueous mixtures in solvent cluster forming conditions. The results indicate that the presence of aromatic residues Y and W and their position in the sequence plays an important role in self-assembly. We observe the formation of amyloid fibrils and other self-assembled structures such as spheres, rings and beads. Our results indicate that 20% HFIP is more favourable for amyloid fibril formation as compared to 20% TFE, when F is replaced with Y or W. The dissolution of peptides in DMSO followed by evaporation of solvent and dissolution in water appears to greatly influence peptide conformation, morphology and cross-β content of self-assembled structures. Our study shows that positioning of aromatic residues F, Y and W have an important role in directing self-assembly of the peptides.     

An analysis of the interactions between folic acid and aromatic guest molecules

The formation of complexes between folate and therapeutic drug molecules is well known. In this work, we attempted to elucidate the role of the aromatic rings of folate and drug molecules in interactions between both of these molecules. A detailed molecular simulation study was carried out to explore the associative behavior of folic acid with phenylalanine and tyrosine, which show fluorescence emission following the excitation of these molecules at 257 nm and 274 nm, respectively. Therefore, studies of fluorescence emission from phenylalanine and tyrosine were performed in this work. The results of these studies indicated that folic acid associates with phenylalanine and tyrosine with binding constants ranging from 1.46 × 10⁴ to 2.66 × 10⁴ M^?1. X-ray diffraction studies suggested that folic acid self-assembly is maintained in the presence of associative interactions of the folic acid with guest molecules. These results demonstrate that the aromatic rings in the structures of the folic acid and the therapeutic drug play an important role in the encapsulation of guest molecules through folate self-assembly.     

Stimuli responsive self-assembled hydrogel of a low molecular weight free dipeptide with potential for tunable drug delivery

Bottom-up fabrication by molecular self-assembly is now widely recognized as a potent method for generating interesting and functional nano- and mesoscale structures. Hydrogels from biocompatible molecules are an interesting class of mesoscale assemblies with potential biomedical applications. The self-assembly of a proteolysis resistant aromatic dipeptide containing a conformational constraining residue (DeltaPhe) into a stable hydrogel has been studied in this work. The reported dipeptide has free -N and -C termini. The hydrogel was self-supportive, was fractaline in nature, and possessed high mechanical strength. It was responsive to environmental conditions like pH, temperature, and ionic strength. The gel matrix could encapsulate and release bioactive molecules in a sustained manner. The described hydrogel showed no observable cytotoxicity to the HeLa and L929 cell lines in culture.     

One-dimensional self-assembly of a rational designed beta-structure peptide

Fabricating various nanostructures based on the self-assembly of diverse biological molecules is now of great interest to the field of bionanotechnology. In this study, we report a de novo designed peptide (T1) with a preferential beta-hairpin forming property that can spontaneously assemble into nanofibrils in ultrapure water. The nanofibrils assembled by T1 could grow up to tens of microns in length with a left-handed helical twist and an average height of 4.9 +/- 0.9 nm. Moreover, protofilaments and nucleus structures both with a similar height of 1.4 +/- 0.2 nm were observed during fibrilization as well as via sonication of the mature nanofibrils. A typical conformational transition from random coil to beta-structure was observed in association with the fibrilization. Molecular modeling of T1 assemblies displayed that the beta-hairpin molecules organize in a parallel fashion in which the beta-strands align in an antiparallel fashion and each adjoining beta-strand runs left-handed twist at about 2.9 degrees with respect to the one located before it along the fibrillar axis. It also revealed that the maximum thickness of the assembly intermediate, the helical tape structure, is about 1.4 nm and four tapes can further assemble into a fibril with a diameter of about 4.1 nm. Taken together the results obtained by AFM, CD, and molecular modeling, T1 fibrilization probably undergoes a hierarchy approach, in which the aromatic stacking and the electrostatic interactions between the assembled structures are most likely the two major factors directing the one-dimensional self-assembly. Based on these studies, we propose T1 can be used as a model peptide to investigate the beta-sheet based self-assembly process and could be a potential bioorganic template to develop functional materials.     

Inhibition of amyloid-β aggregation by coumarin analogs can be manipulated by functionalization of the aromatic center

Aggregation of the amyloid-β protein (Aβ) plays a pathogenic role in the progression of Alzheimer's disease, and small molecules that attenuate Aβ aggregation have been identified toward a therapeutic strategy that targets the disease's underlying cause. Compounds containing aromatic structures have been repeatedly reported as effective inhibitors of Aβ aggregation, but the functional groups that influence inhibition by these aromatic centers have been less frequently explored. The current study identifies analogs of naturally occurring coumarin as novel inhibitors of Aβ aggregation. Derivatization of the coumarin structure is shown to affect inhibitory capabilities and to influence the point at which an inhibitor intervenes within the nucleation dependent Aβ aggregation pathway. In particular, functional groups found within amyloid binding dyes, such as benzothiazole and triazole, can improve inhibition efficacy. Furthermore, inhibitor intervention at early or late stages within the amyloid aggregation pathway is shown to correlate with the ability of these functional groups to recognize and bind amyloid species that appear either early or late within the aggregation pathway. These results demonstrate that functionalization of small aromatic molecules with recognition elements can be used in the rational design of Aβ aggregation inhibitors to not only enhance inhibition but to also manipulate the inhibition mechanism.     

Origin of amphiphilic molecules and their role in primary structure formation

Attempts to solve two fundamental questions are described: the first concerns which mechanisms were responsible for the self-assembly of membrane structures on the prebiotic Earth, and the second concerns the routes by which considerable amounts of membrane amphiphiles formed from simpler hydrocarbons. The physicochemical properties of several amphiphilic compounds extracted from the Murchison carbonaceous chondrite were studied, using infra-red and fluorescent spectroscopy, measurements of surface activity, chromato-mass spectrometry, and polarization and electron microscopy. The results supported previous observations that amphiphilic and aromatic hydrocarbons were present in significant quantities, and the first demonstration of surface activity among a number of acidic derivatives of hydrocarbons is reported. In addition, one fraction of the surface-active compounds can form bilayer structures, showing that membranes could have self-assembled on the prebiotic Earth. Photochemical oxidation of hydrocarbons is shown to be a likely source of the amphiphilic molecules required for the self-assembly of primary membrane structures.     

NMR resonance assignments for the class II GTP binding RNA aptamer in complex with GTP

The structures of RNA-aptamer-ligand complexes solved in the last two decades were instrumental in realizing the amazing potential of RNA for forming complex tertiary structures and for molecular recognition of small molecules. For GTP as ligand the sequences and secondary structures for multiple families of aptamers were reported which differ widely in their structural complexity, ligand affinity and ligand functional groups involved in RNA-binding. However, for only one of these families the structure of the GTP-RNA complex was solved. In order to gain further insights into the variability of ligand recognition modes we are currently determining the structure of another GTP-aptamer—the so-called class II aptamer—bound to GTP using NMR-spectroscopy in solution. As a prerequisite for a full structure determination, we report here ¹H, ¹³C, ¹⁵N and partial ³¹P-NMR resonance assignments for the class II GTP-aptamer bound to GTP.     

Self-assembly of the octapeptide lanreotide and lanreotide-based derivatives: the role of the aromatic residues.

We investigated the spectroscopic properties of the aromatic residues in a set of octapeptides with various self-assembly properties. These octapeptides are based on lanreotide, a cyclic peptide analogue of somatostatin-14 that spontaneously self-assembles into very long and monodisperse hollow nanotubes. A previous study on these lanreotide-based derivatives has shown that the disulfide bridge, the peptide hairpin conformation and the aromatic residues are involved in the self-assembly process and that modification of these properties either decreases the self-assembly propensity or modifies the molecular packing resulting in different self-assembled architectures. In this study we probed the local environment of the aromatic residues, naphthyl-alanine, tryptophan and tyrosine, by Raman and fluorescence spectroscopy, comparing nonassembled peptides at low concentrations with the self-assembled ones at high concentrations. As expected, the spectroscopic characteristics of the aromatic residues were found to be sensitive to the peptide-peptide interactions. Among the most remarkable features we could record a very unusual Raman spectrum for the tyrosine of lanreotide in relation to its propensity to form H-bonds within the assemblies. In Lanreotide nanotubes, and also in the supramolecular architectures formed by its derivatives, the tryptophan side chain is water-exposed. Finally, the low fluorescence polarization of the peptide aggregates suggests that fluorescence energy transfer occurs within the nanotubes.     

Halogenation Generates Effective Modulators of Amyloid-Beta Aggregation and Neurotoxicity

Halogenation of organic compounds plays diverse roles in biochemistry, including selective chemical modification of proteins and improved oral absorption/blood-brain barrier permeability of drug candidates. Moreover, halogenation of aromatic molecules greatly affects aromatic interaction-mediated self-assembly processes, including amyloid fibril formation. Perturbation of the aromatic interaction caused by halogenation of peptide building blocks is known to affect the morphology and other physical properties of the fibrillar structure. Consequently, in this article, we investigated the ability of halogenated ligands to modulate the self-assembly of amyloidogenic peptide/protein. As a model system, we chose amyloid-beta peptide (Aβ), which is implicated in Alzheimer’s disease, and a novel modulator of Aβ aggregation, erythrosine B (ERB). Considering that four halogen atoms are attached to the xanthene benzoate group in ERB, we hypothesized that halogenation of the xanthene benzoate plays a critical role in modulating Aβ aggregation and cytotoxicity. Therefore, we evaluated the modulating capacities of four ERB analogs containing different types and numbers of halogen atoms as well as fluorescein as a negative control. We found that fluorescein is not an effective modulator of Aβ aggregation and cytotoxicity. However, halogenation of either the xanthenes or benzoate ring of fluorescein substantially enhanced the inhibitory capacity on Aβ aggregation. Such Aβ aggregation inhibition by ERB analogs except rose bengal correlated well to the inhibition of Aβ cytotoxicity. To our knowledge, this is the first report demonstrating that halogenation of aromatic rings substantially enhance inhibitory capacities of small molecules on Aβ-associated neurotoxicity via Aβ aggregation modulation.     

Two crystal structures of Trichoderma reesei hydrophobin HFBI--the structure of a protein amphiphile with and without detergent interaction

Hydrophobins are small fungal proteins that are highly surface active and possess a unique ability to form amphiphilic membranes through spontaneous self-assembly. The first crystal structure of a hydrophobin, Trichoderma reesei HFBII, revealed the structural basis for the function of this amphiphilic protein--a patch consisting of hydrophobic side chains on the protein surface. Here, the crystal structures of a native and a variant T. reesei hydrophobin HFBI are presented, revealing the same overall structure and functional hydrophobic patch as in the HFBII structure. However, some structural flexibility was found in the native HFBI structure: The asymmetric unit contained four molecules, and, in two of these, an area of seven residues was displaced as compared to the two other HFBI molecules and the previously determined HFBII structure. This structural change is most probably induced by multimer formation. Both the native and the N-Cys-variant of HFBI were crystallized in the presence of detergents, but an association between the protein and a detergent was only detected in the variant structure. There, the molecules were arranged into an extraordinary detergent-associated octamer and the solvent content of the crystals was 75%. This study highlights the conservation of the fold of class II hydrophobins in spite of the low sequence identity and supports our previous suggestion that concealment of the hydrophobic surface areas of the protein is the driving force in the formation of multimers and monolayers in the self-assembly process.     

Mechanisms of amyloid fibril self-assembly and inhibition. Model short peptides as a key research tool

The formation of amyloid fibrils is associated with various human medical disorders of unrelated origin. Recent research indicates that self-assembled amyloid fibrils are also involved in physiological processes in several micro-organisms. Yet, the molecular basis for the recognition and self-assembly processes mediating the formation of such structures from their soluble protein precursors is not fully understood. Short peptide models have provided novel insight into the mechanistic issues of amyloid formation, revealing that very short peptides (as short as a tetrapeptide) contain all the necessary molecular information for forming typical amyloid fibrils. A careful analysis of short peptides has not only facilitated the identification of molecular recognition modules that promote the interaction and self-assembly of fibrils but also revealed that aromatic interactions are important in many cases of amyloid formation. The realization of the role of aromatic moieties in fibril formation is currently being used to develop novel inhibitors that can serve as therapeutic agents to treat amyloid-associated disorders.     

Fibrous architectures and organogels of tris(phenylethynylphenyl)adamantane molecules with amino acid moieties: their solvato-controlled helicity induction

Non-disk-shaped molecules self-assembled to form columnar-type helical aggregates with gel ability through π-stacking interactions among the central tris(phenylethynylphenyl)adamantane moieties, hydrogen-bonding interactions among the alanine parts with amide groups, and van der Waals interactions among the alkyl groups in nonpolar n-alkanes. The structural analyses of fibrous architectures with helicity were examined by FTIR, UV-Vis, and circular dichroism (CD) spectroscopy and FE-SEM measurements. In contrast, the formation of fibrous structures was observed from adamantane-based tripodal molecules due to solvophobic interactions in polar EtOH, which showed no detectable Cotton effect in the CD measurement, indicating the induction of solvato-controlled helicity in the self-assembly process.