Microscopic vibrational circular dichroism on the forewings of a European hornet: heterogenous sequences of protein domains with different secondary structures

We developed a microscopic scanning for vibrational circular dichroism (VCD) spectroscopy in which a quantum cascade laser is equipped with a highly focused infrared light source to attain a spatial resolution of 100 μm. This system was applied to the forewing of a European hornet to reveal how the protein domains are organised. Two-dimensional patterns were obtained from the VCD signals with steps of 100 μm. We scanned the 1500-1740 cm-1 wavenumber range, which covers amide I and II absorptions. Zone sequenced α-helical and β-sheet domains within an area of 200 μm2 in membranes close to where two veins cross. The sign of the VCD signal at 1650 cm-1 changed from positive to negative when probed along the zone axis, intermediated by the absence of VCD activity. The significance of this zone is discussed from the viewpoint of the mechanical properties required for flying motion. These features are unattainable using conventional FTIR (Fourier transform infrared) or FT-VCD methods with a spatial resolution of ∼10 mm2.

Salt-induced Fmoc-tripeptide supramolecular hydrogels: a combined experimental and computational study of the self-assembly

Delving into the mechanism behind the molecular interactions at the atomic level of short-sequence peptides plays a key role in the development of nanomaterials with specific structure-property-function relationships from a bottom-up perspective. Due to their poor water solubility, the self-assembly of Fmoc-bearing peptides is usually induced by dissolution in an organic solvent, followed by a dilution step in water, pH changes, and/or a heating-cooling process. Herein, we report a straightforward methodology for the gelation of Fmoc-FFpY (F: phenylalanine; Y: tyrosine; and p: PO42-), a negatively charged tripeptide, in NaCl solution. The electrostatic interactions between Fmoc-FFpY and Na+ ions give rise to different nanofibrillar hydrogels with rheological properties and nanofiber sizes modulated by the NaCl concentration in pure aqueous media. Initiated by the electrostatic interactions between the peptide phosphate groups and the Na+ ions, the peptide self-assembly is stabilized thanks to hydrogen bonds between the peptide backbones and the π-π stacking of aromatic Fmoc and phenyl units. The hydrogels showed self-healing and thermo-responsive properties for potential biomedical applications. Molecular dynamics simulations from systems devoid of prior training not only confirm the aggregation of peptides at a critical salt concentration and the different interactions involved, but also corroborate the secondary structure of the hydrogels at the microsecond timescale. It is worth highlighting the remarkable achievement of reproducing the morphological behavior of the hydrogels using atomistic simulations. To our knowledge, this study is the first to report such a correspondence.

Development, Validation, and Applications of Nonbonded Interaction Parameters between Coarse-Grained Amino Acid and Water Models

Interactions between amino acids and water play an important role in determining the stability and folding/unfolding, in aqueous solution, of many biological macromolecules, which affects their function. Thus, understanding the molecular-level interactions between water and amino acids is crucial to tune their function in aqueous solutions. Herein, we have developed nonbonded interaction parameters between the coarse-grained (CG) models of 20 amino acids and the one-site CG water model. The nonbonded parameters, represented using the 12-6 Lennard Jones (LJ) potential form, have been optimized using an artificial neural network (ANN)-assisted particle swarm optimization (PSO) (ANN-assisted PSO) method. All-atom (AA) molecular dynamics (MD) simulations of dipeptides in TIP3P water molecules were performed to calculate the Gibbs hydration free energies. The nonbonded force-field (FF) parameters between CG amino acids and the one-site CG water model were developed to accurately reproduce these energies. Furthermore, to test the transferability of these newly developed parameters, we calculated the hydration free energies of the analogues of the amino acid side chains, which showed good agreement with reported experimental data. Additionally, we show the applicability of these models by performing self-assembly simulations of peptide amphiphiles. Overall, these models are transferable and can be used to study the self-assembly of various biomaterials and biomolecules to develop a mechanistic understanding of these processes.

Self-Assembly of Phenylalanine-Leucine, Leucine-Phenylalanine, and Cyclo(-leucine-phenylalanine) Dipeptides through Simulations and Experiments

For over two decades, peptide self-assembly has been the focus of attention and a great source of inspiration for biomedical and nanotechnological applications. The resulting peptide nanostructures and their properties are closely related to the information encoded within each peptide building block, their sequence, and their modes of self-organization. In this work. we assess the behavior and differences between the self-association of the aromatic-aliphatic Phe-Leu dipeptide compared to its retro-sequence Leu-Phe and cyclic Cyclo(-Leu-Phe) counterparts, using a combination of simulation and experimental methods. Detailed all-atom molecular dynamics (MD) simulations offer a quantitative prediction at the molecular level of the conformational, dynamical and structural properties of the peptides' self-assembly, while field emission scanning electron microscopy (FESEM) experiments allow microscopic observation of the self-assembled end-structures. The complementarity and qualitative agreement between the two methods not only highlights the differences between the self-assembly propensity of cyclic and linear retro-sequence peptides but also sheds light on underlying mechanisms of self-organization. The self-assembling propensity was found to follow the order: Cyclo(-Leu-Phe) > Leu-Phe > Phe-Leu.

Atomistic Pictures of Self-Assembled Helical Peptide Nanofibers

Spontaneous self-assembly of peptides has been at the forefront of supramolecular chemistry and materials science research over the last two decades. Despite the wealth of information on the morphology of the assembled objects, atomic resolution details of molecular arrangements inside them are largely unknown. In this paper, we investigated non-covalent assemblies of zwitterionic l-phenylalanine tripeptides in water using all-atom explicit-solvent molecular dynamics computer simulations. Our studies produced atomistic pictures of spontaneously assembled nanofibers composed of hundreds of peptide molecules. The dimensions of the nanofibers varied from 10 to 18 nm, with irregular helical twists along the long axes. Previously published experimental data, acquired under similar conditions, provided direct validation of the fibrous morphology and indirect support for the non-trivial helicity observed in our simulations. Quantitative analyses of peptide-water and peptide-peptide interactions revealed heterogeneous local environments of molecules across the nanometer length scales. The combination of electrostatic, hydrogen bonding, van der Waals, and hydrophobic interactions, adopted by a single molecule, was dependent on its relative position inside the fiber. Despite the presence of three hydrophobic phenyl groups, very few molecules were found to be completely shielded from the surrounding water, indicating a subtle role of the hydrophobic effect. Limited conformational flexibility of the tripeptide, along with bare electrostatic interactions, appeared to play a crucial role in the emergence of fibrous morphology of the nanostructures. Our analyses led us to formulate plausible qualitative explanations of the assembly behavior in terms of thermodynamic driving forces and kinetic considerations. We established a clear relationship between details of chemical interactions operating within few molecules and characteristics of the self-assembled states at much longer length scales.

How the Choice of Force-Field Affects the Stability and Self-Assembly Process of Supramolecular CTA Fibers

In recent years, computational methods have become an essential element of studies focusing on the self-assembly process. Although they provide unique insights, they face challenges, from which two are the most often mentioned in the literature: the temporal and spatial scale of the self-assembly. A less often mentioned issue, but not less important, is the choice of the force-field. The repetitive nature of the supramolecular structure results in many similar interactions. Consequently, even a small deviation in these interactions can lead to significant energy differences in the whole structure. However, studies comparing different force-fields for self-assembling systems are scarce. In this article, we compare molecular dynamics simulations for trifold hydrogen-bonded fibers performed with different force-fields, namely GROMOS, CHARMM General Force Field (CGenFF), CHARMM Drude, General Amber Force-Field (GAFF), Martini, and polarized Martini. Briefly, we tested the force-fields by simulating: (i) spontaneous self-assembly (none form a fiber within 500 ns), (ii) stability of the fiber (observed for CHARMM Drude, GAFF, MartiniP), (iii) dimerization (observed for GROMOS, GAFF, and MartiniP), and (iv) oligomerization (observed for CHARMM Drude and MartiniP). This system shows that knowledge of the force-field behavior regarding interactions in oligomer and larger self-assembled structures is crucial for designing efficient simulation protocols for self-assembling systems.

Self-assembly of an in silico designed dipeptide derivative to obtain photo-responsive vesicles

Photo-responsive vesicles self-assembled from in silico designed peptide derivatives were investigated using coarse-grained molecular dynamics simulations.

Theoretical Study of Macrocyclic Host Molecules: From Supramolecular Recognition to Self-Assembly

Supramolecular chemistry focuses on molecular recognition and self-assembly of various building blocks through weak non-covalent interactions, including anion-π, hydrogen bond (HB), hydrophobic interactions, van der Waals (vdW) interactions, etc, which...

Computational Insights into the Aggregation Pathway of Self-Assembled Nanotubules

We performed molecular dynamics simulations of self-assembled supramolecular nanotubules constructed from amphiphiles with bent-shaped rods. By systematically examining the structure from dimeric aggregates to the fully developed nanotubule, we identified the basic building block of the nanotubule and the optimal dimensions of its stable structure which are consistent with experimental findings. Moreover, we demonstrate that the cooperative interplay of different interactions drives aggregation by selecting and stabilizing the optimal self-assembled structures for various intermediates through a complex pathway. Additionally, contraction of the nanotubule, which accompanies the dehydration process, was observed upon heating. It is suggested that the optimal stability of the self-assembled aggregates is achieved by balancing entropic and enthalpic contributions, of which the ratio is a critical factor that drives the aggregation pathway.

Self-assembled peptide and protein nanostructures for anti-cancer therapy: Targeted delivery, stimuli-responsive devices and immunotherapy

Self-assembled peptides and proteins possess tremendous potential as targeted drug delivery systems and key applications of these well-defined nanostructures reside in anti-cancer therapy. Peptides and proteins can self-assemble into nanostructures of diverse sizes and shapes in response to changing environmental conditions such as pH, temperature, ionic strength, as well as host and guest molecular interactions; their countless benefits include good biocompatibility and high loading capacity for hydrophobic and hydrophilic drugs. These self-assembled nanomaterials can be adorned with functional moieties to specifically target tumor cells. Stimuli-responsive features can also be incorporated with respect to the tumor microenvironment. This review sheds light on the growing interest in self-assembled peptides and proteins and their burgeoning applications in cancer treatment and immunotherapy.

Solid-state packing dictates the unexpected solubility of aromatic peptides

The understanding and prediction of the solubility of biomolecules, even of the simplest ones, reflect an open question and unmet need. Short aromatic tripeptides are among the most highly aggregative biomolecules. However, in marked contrast, Ala-Phe-Ala (AFA) was surprisingly found to be non-aggregative and could be solubilized at millimolar concentrations. Here, aiming to uncover the underlying molecular basis of its high solubility, we explore in detail the solubility, aggregation propensity, and atomic-level structure of the tripeptide. We demonstrate an unexpectedly high water solubility of AFA reaching 672 mM, two orders of magnitude higher than reported previously. The single crystal structure reveals an anti-parallel β sheet conformation devoid of any aromatic interactions. This study provides clear mechanistic insight into the structural basis of solubility and suggests a simple and feasible tool for its estimation, bearing implications for design of peptide drugs, peptides materials, and advancement of peptide nanotechnology.

Fluorinated peptide biomaterials

Fluorinated compounds, while rarely used by nature, are emerging as fundamental ingredients in biomedical research, with applications in drug discovery, metabolomics, biospectroscopy, and, as the focus of this review, peptide/protein engineering. Leveraging the fluorous effect to direct peptide assembly has evolved an entirely new class of organofluorine building blocks from which unique and bioactive materials can be constructed. Here, we discuss three distinct peptide fluorination strategies used to design and induce peptide assembly into nano-, micro-, and macrosupramolecular states that potentiate high-ordered organization into material scaffolds. These fluorine-tailored peptide assemblies employ the unique fluorous environment to boost biofunctionality for a broad range of applications, from drug delivery to antibacterial coatings. This review provides foundational tactics for peptide fluorination and discusses the utility of these fluorous-directed hierarchical structures as material platforms in diverse biomedical applications.

Self-assembly of diphenylalanine peptides on graphene via detailed atomistic simulations

The self-assembly of diphenylalanine peptides (FF) on a graphene layer, in aqueous solution, is investigated, through all atom molecular dynamics simulations. Two interfacial systems are studied, with different concentrations of dipeptides and the results are compared with an aqueous solution of FF at room temperature. Corresponding length and time scales of the formed structures are quantified providing important insight into the adsorption mechanism of FF onto the graphene surface. A hierarchical formation of FF structures is observed involving two sequential processes: first, a stabilized interfacial layer of dipeptides onto the graphene surface is formulated, which next is followed by the development of a structure of self-aggregated dipeptides on top of this layer. The whole procedure is completed in almost 200 ns, whereas self-assembly in the system without graphene is accomplished much faster; in less than 50 ns cylindrical structures, the microscopic signal of the macroscopic fibrillar ones, are formed. Strong π-π* interactions between FF and the graphene lead to a parallel orientation to the graphene layer of the phenyl rings within a characteristic time of 80 ns, similar to the one indicated by the time evolution of the number of adsorbed FF atoms at the surface. Reduction in the number of hydrogen bonds between FF peptides is observed because of the graphene layer, since it disturbs their self-assembly propensity. The self-assembly of dipeptides and their adsorption onto the graphene surface destruct the hydrogen bond network of water, in the vicinity of FF, however, the total number of hydrogen bonds in all systems increases, promoting the formed structures.

In search of a novel chassis material for synthetic cells: emergence of synthetic peptide compartment

Giant lipid vesicles have been used extensively as a synthetic cell model to recapitulate various life-like processes, including in vitro protein synthesis, DNA replication, and cytoskeleton organization. Cell-sized lipid vesicles are mechanically fragile in nature and prone to rupture due to osmotic stress, which limits their usability. Recently, peptide vesicles have been introduced as a synthetic cell model that would potentially overcome the aforementioned limitations. Peptide vesicles are robust, reasonably more stable than lipid vesicles and can withstand harsh conditions including pH, thermal, and osmotic variations. This mini-review summarizes the current state-of-the-art in the design, engineering, and realization of peptide-based chassis materials, including both experimental and computational work. We present an outlook for simulation-aided and data-driven design and experimental realization of engineered and multifunctional synthetic cells.

Self-assembly of Alanine-Isoleucine and Isoleucine-Isoleucine Dipeptides through Atomistic Simulations and Experiments

A detailed investigation of the structural and conformational properties of alanine-isoleucine (Ala-Ile) and isoleucine-isoleucine (Ile-Ile) dipeptides is presented in water and in methanol solvents. We propose a consistent combination of complementary simulation and experimental methods, covering a broad range of length and time scales, from the very short (i.e., atomic level), via all-atom molecular dynamics (MD) simulations, up to the macroscopic one, via scanning electron microscopy (SEM) experiments. The examined samples from both simulations and experiment cover a board range of concentrations since these are usually in different concentration windows (i.e., high values in simulations vs low values in experiments). In the present study, there is an overlapping concentration regime and a qualitative agreement between simulation and experimental results is observed. The effect of temperature on the formed structures is found to be small, from both simulation and experiments, when temperature varies from 278 to 300 K. Furthermore, the differences of Ala-Ile and Ile-Ile dipeptides from dialanine (Ala-Ala) and diphenylalanine (Phe-Phe) dipeptides in similar conditions are highlighted. Based on various measures, the strength of the self-assembly propensity of the four dipeptides in aqueous solutions attains the following order: Phe-Phe > Ala-Ile > Ala-Ala > Ile-Ile.

Role of aromatic amino acids in amyloid self-assembly

Amyloids are proteins of a cross-β structure found as deposits in several diseases and also in normal tissues (nails, spider net, silk). Aromatic amino acids are frequently found in amyloid deposits. Although they are not indispensable, aromatic amino acids, phenylalanine, tyrosine and tryptophan, enhance significantly the kinetics of formation and thermodynamic stability, while tape or ribbon-like morphology is represented in systems with experimentally detected π-π interactions between aromatic rings. Analysis of geometries and energies of the amyloid PDB structures indicate the prevalence of aromatic-nonaromatic interactions and confirm that aromatic-aromatic interactions are not crucial for the amyloid formation.

Expanding the structural diversity of peptide assemblies by coassembling dipeptides with diphenylalanine

Molecular self-assembly is a bottom-up approach to fabricate novel supramolecular structures. While the structural diversity obtained by the use of a single type of building block is limited, coassembly of different peptides has recently evolved as an extended strategy to expand the diversity of peptide nanoarchitectures. Here we systematically investigate the coassembly of diphenylalanine (FF) with each one of the 399 non-FF dipeptides by micro-second molecular dynamics simulations. Our simulations show that dipeptides, by coassembling with FF, display a greatly enhanced aggregation propensity and a significantly expanded structural diversity. Regular-shaped vesicles, single- or multi-cavity assemblies, and planar sheets are formed by coassembly of FF with different types of non-FF dipeptides, which are rarely observed in self-assemblies of non-FF dipeptides. Interaction analyses reveal that the formation of these varied structures is attributed to a delicate balance between aromatic stacking, hydrophobic, and electrostatic repulsion interactions. This study provides structural and mechanistic insights into the coassembly of FF and non-FF dipeptides, thus offering a possible way to achieve a controllable design of bionanomaterials through FF-involved dipeptide coassembly.

Computational Nanoscopy of Tight Junctions at the Blood-Brain Barrier Interface

The selectivity of the blood-brain barrier (BBB) is primarily maintained by tight junctions (TJs), which act as gatekeepers of the paracellular space by blocking blood-borne toxins, drugs, and pathogens from entering the brain. The BBB presents a significant challenge in designing neurotherapeutics, so a comprehensive understanding of the TJ architecture can aid in the design of novel therapeutics. Unraveling the intricacies of TJs with conventional experimental techniques alone is challenging, but recently developed computational tools can provide a valuable molecular-level understanding of TJ architecture. We employed the computational methods toolkit to investigate claudin-5, a highly expressed TJ protein at the BBB interface. Our approach started with the prediction of claudin-5 structure, evaluation of stable dimer conformations and nanoscale assemblies, followed by the impact of lipid environments, and posttranslational modifications on these claudin-5 assemblies. These led to the study of TJ pores and barriers and finally understanding of ion and small molecule transport through the TJs. Some of these in silico, molecular-level findings, will need to be corroborated by future experiments. The resulting understanding can be advantageous towards the eventual goal of drug delivery across the BBB. This review provides key insights gleaned from a series of state-of-the-art nanoscale simulations (or computational nanoscopy studies) performed on the TJ architecture.

Nucleation and Growth of Amino Acid and Peptide Supramolecular Polymers through Liquid-Liquid Phase Separation

The transition of peptides and proteins from the solution phase into fibrillar structures is a general phenomenon encountered in functional and aberrant biology and is increasingly exploited in soft materials science. However, the fundamental molecular events underpinning the early stages of their assembly and subsequent growth have remained challenging to elucidate. Here, we show that liquid-liquid phase separation into solute-rich and solute-poor phases is a fundamental step leading to the nucleation of supramolecular nanofibrils from molecular building blocks, including peptides and even amphiphilic amino acids. The solute-rich liquid droplets act as nucleation sites, allowing the formation of thermodynamically favorable nanofibrils following Ostwald's step rule. The transition from solution to liquid droplets is entropy driven while the transition from liquid droplets to nanofibrils is mediated by enthalpic interactions and characterized by structural reorganization. These findings shed light on how the nucleation barrier toward the formation of solid phases can be lowered through a kinetic mechanism which proceeds through a metastable liquid phase.

Molecular Model for the Self-Assembly of the Cyclic Lipodepsipeptide Pseudodesmin A

Self-assembly of peptides into supramolecular structures represents an active field of research with potential applications ranging from material science to medicine. Their study typically involves the application of a large toolbox of spectroscopic and imaging techniques. However, quite often, the structural aspects remain underexposed. Besides, molecular modeling of the self-assembly process is usually difficult to handle, since a vast conformational space has to be sampled. Here, we have used an approach that combines short molecular dynamics simulations for peptide dimerization and NMR restraints to build a model of the supramolecular structure from the dimeric units. Experimental NMR data notably provide crucial information about the conformation of the monomeric units, the supramolecular assembly dimensions, and the orientation of the individual peptides within the assembly. This in silico/in vitro mixed approach enables us to define accurate atomistic models of supramolecular structures of the bacterial cyclic lipodepsipeptide pseudodesmin A.

Orthogonally Stimulated Assembly/Disassembly of Depsipeptides by Rational Chemical Design

Controlling the assembly and disassembly of cross-β-sheet-forming peptides is one of the predominant challenges for this class of supramolecular material. As they constitute a continuously propagating material, every atomic change can be exploited to bring about distinct responses at the architectural level. We report herein that, by using rational chemical design, serine and methionine can both be used as orthogonal chemical triggers to signal assembly/disassembly through their corresponding stimuli. Serine is used to construct an ester-bond oligopeptide that can undergo O,N-acyl rearrangement, whereas methionine is sensitive to oxidation by H2 O2 . Using the example peptide sequence, KIKISQINM, we demonstrate that assembly and disassembly can be independently controlled on demand.

Supramolecular Tripeptide Hydrogel Assembly with 5-Fluorouracil

In this work, we present Thioflavin T fluorescence, transmission electron microscopy (TEM), circular dichroism (CD), Fourier-transformed infrared (FT-IR), and oscillatory rheometry studies applied to an antineoplastic drug, 5-fluorouracil (5-FU), embedded in a heterochiral tripeptide hydrogel to obtain a drug delivery supramolecular system. The release of 5-fluorouracil was monitored over time by reverse-phase high-performance liquid chromatography (HPLC) and its interaction with the tripeptide assemblies was probed by all-atom molecular dynamics simulations.

Stable and Biocompatible Monodispersion of C60 in Water by Peptides

The lack of solubility in water and the formation of aggregates hamper many opportunities for technological exploitation of C₆₀. Here, different peptides were designed and synthesized with the aim of monomolecular dispersion of C₆₀ in water. Phenylalanines were used as recognizing moieties, able to interact with C₆₀ through π-π stacking, while a varying number of glycines were used as spacers, to connect the two terminal phenylalanines. The best performance in the dispersion of C₆₀ was obtained with the FGGGF peptidic nanotweezer at a pH of 12. A full characterization of this adduct was carried out. The peptides disperse C₆₀ in water with high efficiency, and the solutions are stable for months both in pure water and in physiological environments. NMR measurements demonstrated the ability of the peptides to interact with C₆₀. AFM measurements showed that C₆₀ is monodispersed. Electrospray ionization mass spectrometry determined a stoichiometry of C₆₀@(FGGGF)₄. Molecular dynamics simulations showed that the peptides assemble around the C₆₀ cage, like a candy in its paper wrapper, creating a supramolecular host able to accept C₆₀ in the cavity. The peptide-wrapped C₆₀ is fully biocompatible and the C₆₀ "dark toxicity" is eliminated. C₆₀@(FGGGF)₄ shows visible light-induced reactive oxygen species (ROS) generation at physiological saline concentrations and reduction of the HeLa cell viability in response to visible light irradiation.

Elucidating Self-Assembling Peptide Aggregation via Morphoscanner: A New Tool for Protein-Peptide Structural Characterization

Self-assembling and molecular folding are ubiquitous in Nature: they drive the organization of systems ranging from living creatures to DNA molecules. Elucidating the complex dynamics underlying these phenomena is of crucial importance. However, a tool for the analysis of the various phenomena involved in protein/peptide aggregation is still missing. Here, an innovative software is developed and validated for the identification and visualization of b-structuring and b-sheet formation in both simulated systems and crystal structures of proteins and peptides. The novel software suite, dubbed Morphoscanner, is designed to identify and intuitively represent b-structuring and b-sheet formation during molecular dynamics trajectories, paying attention to temporary strand-strand alignment, suboligomer formation and evolution of local order. Self-assembling peptides (SAPs) constitute a promising class of biomaterials and an interesting model to study the spontaneous assembly of molecular systems in vitro. With the help of coarse-grained molecular dynamics the self-assembling of diverse SAPs is simulated into molten aggregates. When applied to these systems, Morphoscanner highlights different b-structuring schemes and kinetics related to SAP sequences. It is demonstrated that Morphoscanner is a novel versatile tool designed to probe the aggregation dynamics of self-assembling systems, adaptable to the analysis of differently coarsened simulations of a variety of biomolecules.

Evidence for Prenucleated Fibrilogenesis of Acid-Mediated Self-Assembling Oligopeptides via Molecular Simulation and Fluorescence Correlation Spectroscopy

An important step in controlling biomimetic amyloid systems is understanding the self-assembly reaction kinetics. We are interested in a family of such materials characterized by symmetric sequences of amino acids flanking a π-conjugated functional core. Many of these materials rapidly self-assemble into long fibers upon protonation in an acidic environment. Despite extensive investigation of these materials' properties, little is yet understood regarding their reaction kinetics. Based on previous studies, we have chosen DFAG-4T-GAFD as a representative system and conducted molecular dynamics simulations to show that although large-scale assembly is induced by lowering pH, some degree of assembly is thermodynamically favorable in high-pH nonprotonating environments. These results are consistent with findings for other systems such as DFAG-OPV-GAFD. The nonprotonated aggregation also appears to be concentration dependent, occurring at concentrations of 100 nM and above. Single molecule measurements using fluorescence correlation spectroscopy provide experimental support for these computational predictions. We find evidence of spontaneous aggregation in aqueous solutions of peptides with concentrations as low as 100 nM; however, 10 nM solutions appear to be largely homogeneous solutions of unassembled monomer. These results indicate that the simplest explanations for kinetics of acid-mediated assembly-protonation-induced nucleation by monomeric addition followed by subsequent stages of aggregation and elongation-are inappropriate in this system. In fact, the system only exists as pure monomer in very low concentrations, nucleation actually occurs in the absence of protonating elements at concentrations typically used for experiments, and pH triggered assembly proceeds from these preassembled aggregates. Accordingly, triggered assembly must be considered to operate outside the domain of nucleation-dependent models.

Supramolecular Nucleoside-Based Gel: Molecular Dynamics Simulation and Characterization of Its Nanoarchitecture and Self-Assembly Mechanism

Among the diversity of existing supramolecular hydrogels, nucleic acid-based hydrogels are of particular interest for potential drug delivery and tissue engineering applications because of their inherent biocompatibility. Hydrogel performance is directly related to the nanostructure and the self-assembly mechanism of the material, an aspect that is not well-understood for nucleic acid-based hydrogels in general and has not yet been explored for cytosine-based hydrogels in particular. Herein, we use a broad range of experimental characterization techniques along with molecular dynamics (MD) simulation to demonstrate the complementarity and applicability of both approaches for nucleic acid-based gelators in general and propose the self-assembly mechanism for a novel supramolecular gelator, N4-octanoyl-2'-deoxycytidine. The experimental data and the MD simulation are in complete agreement with each other and demonstrate the formation of a hydrophobic core within the fibrillar structures of these mainly water-containing materials. The characterization of the distinct duality of environments in this cytidine-based gel will form the basis for further encapsulation of both small hydrophobic drugs and biopharmaceuticals (proteins and nucleic acids) for drug delivery and tissue engineering applications.

Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments

In bionanotechnology, the field of creating functional materials consisting of bio-inspired molecules, the function and shape of a nanostructure only appear through the assembly of many small molecules together. The large number of building blocks required to define a nanostructure combined with the many degrees of freedom in packing small molecules has long precluded molecular simulations, but recent advances in computational hardware as well as software have made classical simulations available to this strongly expanding field. Here, we review the state of the art in simulations of self-assembling bio-inspired supramolecular systems. We will first discuss progress in force fields, simulation protocols and enhanced sampling techniques using recent examples. Secondly, we will focus on efforts to enable the comparison of experimentally accessible observables and computational results. Experimental quantities that can be measured by microscopy, spectroscopy and scattering can be linked to simulation output either directly or indirectly, via quantum mechanical or semi-empirical techniques. Overall, we aim to provide an overview of the various computational approaches to understand not only the molecular architecture of nanostructures, but also the mechanism of their formation.

Biofunctionalized peptide nanofiber-based composite scaffolds for bone regeneration

Bone tissue had moderate self-healing capabilities, but biomaterial scaffolds were required for the repair of some defects such as large bone defects. Peptide nanofiber scaffolds demonstrated important potential in regenerative medicine. Functional modification and controlled release of signal molecules were two significant approaches to increase the bioactivity of biofunctionalized peptide nanofiber scaffolds, but peptide scaffolds were limited by insufficient mechanical strength. Thus, it was necessary to combine peptide scaffolds with other materials including polymers, hydroxyapatite, demineralized bone matrix (DBM) and metal materials based on the requirement of different bone defects. As the development of peptide-based composite scaffolds continued to evolve, ultimate translation to the clinical environment may allow for improved therapeutic outcomes for bone repair.

Crystalline Dipeptide Nanobelts Based on Solid-Solid Phase Transformation Self-Assembly and Their Polarization Imaging of Cells

Controlled phase transformation involving biomolecular organization to generate dynamic biomimetic self-assembly systems and functional materials is currently an appealing topic of research on molecular materials. Herein, we achieve by ultrasonic irradiation the direct solid-solid transition of bioinspired dipeptide organization from triclinic structured aggregates to  nanofibers and eventually to monoclinic nanobelts with strong polarized luminescence. It is suggested that the locally high temperature and pressure produced by cavitation effects cleaves the hydrophobic, π-π stacking or self-locked intramolecular interactions involved in one phase state and then rearranges the molecular packing to form another well-ordered aromatic dipeptide crystalline structure. Such a sonication-modulated solid-solid phase transition evolution is governed by distinct molecular interactions at different stages of structural organization. The resulting crystalline nanobelts are for the first time applied for polarization imaging of cells, which can be advantageous to directly inspect the uptake and fate of nanoscale delivery platforms without labeling of fluorescent dyes. This finding provides a new perspective to comprehend the dynamic evolution of biomolecular self-organization with energy supply by an external field and open up a facile and versatile approach of using anisotropic nanostructures for polarization imaging of cells and even live organisms in future.

Amphiphile self-assembly dynamics at the solution-solid interface reveal asymmetry in head/tail desorption

Asymmetric dynamics in fundamental adsorption and desorption steps drive self-assembly at solution/solid interface.

Trace Water as Prominent Factor to Induce Peptide Self-Assembly: Dynamic Evolution and Governing Interactions in Ionic Liquids

The interaction between water and biomolecules including peptides is of critical importance for forming high-level architectures and triggering life's functions. However, the bulk aqueous environment has limitations in detecting the kinetics and mechanisms of peptide self-assembly, especially relating to interactions of trace water. With ionic liquids (ILs) as a nonconventional medium, herein, it is discovered that trace amounts of water play a decisive role in triggering self-assembly of a biologically derived dipeptide. ILs provide a suitable nonaqueous environment, enabling us to mediate water content and follow the dynamic evolution of peptide self-assembly. The trace water is found to be involved in the assembly process of dipeptide, especially leading to the formation of stable noncovalent dipeptide oligomers in the early stage of nucleation, as evident by both experimental studies and theoretical simulations. The thermodynamics of the growth process is mainly governed by a synergistic effect of hydrophobic interaction and hydrogen bonds. Each step of assembly presents a different trend in thermodynamic energy. The dynamic evolution of assembly process can be efficiently mediated by changing trace water content. The decisive role of trace water in triggering and mediating self-assembly of biomolecules provides a new perspective in understanding supramolecular chemistry and molecular self-organization in biology.

Thermally Induced Self-Assembly and Cyclization of l-Leucyl-l-Leucine in Solid State

Thermal treatment of oligopeptides is one of the methods for synthesis of organic nanostructures. However, heating may lead not only to self-assembly of the initial molecules, but also to chemical reactions resulting in the formation of new unexpected nanostructures or change in the properties of the existing ones. In the present work, the reaction of cyclization of dipeptide l-leucyl-l-leucine in solid state under heating was studied. The change in morphology of dipeptide thin film and formation of nanostructures after heating was visualized using atomic force microscopy. This method also was used for demonstration of differences in self-assembly of linear and cyclic dipeptides. The chemical structure of reaction product was characterized by NMR spectrometry, FTIR spectroscopy and GC-MS analysis. Kinetic parameters of cyclization were estimated within the approaches of the nonisothermal kinetics ("model-free" kinetics and linear regression methods for detection of topochemical equation). The results of present work are useful for explanation the changes in the properties of nanostructures based on short-chain oligopeptides, notably leucyl-leucine, after thermal treatment, as well as for the synthesis of cyclic oligopeptides.

Backbone Engineered γ-Peptide Amphitropic Gels for Immobilization of Semiconductor Quantum Dots and 2D Cell Culture

We are reporting a spontaneous supramolecular assembly of backbone engineered γ-peptide scaffold and its utility in the immobilization of semiconductor quantum dots and in cell culture. The stimulating feature of this γ-peptide scaffold is that it efficiently gelates both aqueous phosphate buffers and aromatic organic solvents. A comparative and systematic investigation reveals that the greater spontaneous self-aggregation property of γ-peptide over the α- and β-peptide analogues is mainly due to the backbone flexibility, increased hydrophobicity, and π-π stacking of γ-phenylalanine residues. The hydrogels and organogels obtained from the γ-peptide scaffold have been characterized through field emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), FT-IR, circular dichroism (CD), wide-angle X-ray diffraction, and rheometric study. Additionally, the peptide hydrogel has displayed a stimuli-responsive and thixotropic signature, which leads to the injectable hydrogels. 2D cell culture studies using normal and cancer cell lines reveal the biocompatibility of γ-peptide hydrogels. Further, the immobilization of semiconductor core-shell quantum dots in the transparent γ-peptide organogels showed ordered arrangement of quantum dots along the peptide fibrillar network with retaining photophysical property. Overall, γ-peptide scaffolds may serve as potential templates for the design of new functional biomaterials.