Triphenylalanine peptides self-assemble into nanospheres and nanorods that are different from the nanovesicles and nanotubes formed by diphenylalanine peptides

Elastin-Derived Peptide-Based Hydrogels as a Potential Drug Delivery System

A peptide-based hydrogel sequence was computationally predicted from the Ala-rich cross-linked domains of elastin. Three candidate peptides were subsequently synthesised and characterised as potential drug delivery vehicles. The elastin-derived peptides are Fmoc-FFAAAAKAA-NH2, Fmoc-FFAAAKAA-NH2, and Fmoc-FFAAAKAAA-NH2. All three peptide sequences were able to self-assemble into nanofibers. However, only the first two could form hydrogels, which are preferred as delivery systems compared to solutions. Both of these peptides also exhibited favourable nanofiber lengths of at least 1.86 and 4.57 µm, respectively, which are beneficial for the successful delivery and stability of drugs. The shorter fibre lengths of the third peptide (maximum 0.649 µm) could have inhibited their self-assembly into the three-dimensional networks crucial to hydrogel formation.

Tips and Tricks in the Modeling of Supramolecular Peptide Assemblies

Supramolecular peptide assemblies (SPAs) hold promise as materials for nanotechnology and biomedicine. Although their investigation often entails adapting experimental techniques from their protein counterparts, SPAs are fundamentally distinct from proteins, posing unique challenges for their study. Computational methods have emerged as indispensable tools for gaining deeper insights into SPA structures at the molecular level, surpassing the limitations of experimental techniques, and as screening tools to reduce the experimental search space. However, computational studies have grappled with issues stemming from the absence of standardized procedures and relevant crystal structures. Fundamental disparities between SPAs and protein simulations, such as the absence of experimentally validated initial structures and the importance of the simulation size, number of molecules, and concentration, have compounded these challenges. Understanding the roles of various parameters and the capabilities of different models and simulation setups remains an ongoing endeavor. In this review, we aim to provide readers with guidance on the parameters to consider when conducting SPA simulations, elucidating their potential impact on outcomes and validity.

Effect of terahertz waves on the aggregation behavior of neurotransmitters

Understanding the dynamics of neurotransmitters is crucial for unraveling synaptic transmission mechanisms in neuroscience. In this study, we investigated the impact of terahertz (THz) waves on the aggregation of four common neurotransmitters through all-atom molecular dynamics (MD) simulations. The simulations revealed enhanced nicotine (NCT) aggregation under 11.05 and 21.44 THz, with a minimal effect at 42.55 THz. Structural analysis further indicated strengthened intermolecular interactions and weakened hydration effects under specific THz stimulation. In addition, enhanced aggregation was observed at stronger field strengths, particularly at 21.44 THz. Furthermore, similar investigations on epinephrine (EPI), 5-hydroxytryptamine (5-HT), and γ-aminobutyric acid (GABA) corroborated these findings. Notably, EPI showed increased aggregation at 19.05 THz, emphasizing the influence of vibrational modes on aggregation. However, 5-HT and GABA, with charged or hydrophilic functional groups, exhibited minimal aggregation under THz stimulation. The present study sheds some light on neurotransmitter responses to THz waves, offering implications for neuroscience and interdisciplinary applications.

Multiscale, Multiresolution Coarse-Grained Model via a Hybrid Approach: Solvation, Structure, and Self-Assembly of Aromatic Tripeptides

Short aromatic peptides have been observed to assemble into diverse nanostructures, including fibers, tubes, and vesicles, using computational techniques. However, the computational studies have employed top-down coarse-grained (CG) models, which are unable to capture the assembly along with the conformation, packing, and organization of the peptides within the aggregates in a manner that is consistent with the all atom (AA) representation of the molecules. In this study, a hybrid structure- and force-based approach is adapted to develop a bottom-up CG force field of triphenylalanine using reference data from AA trajectories. This approach follows a flexible methodology to approximate the chemical complexity of the underlying AA representation with the chosen CG representation. Two CG models are developed with distinct representations of the aromatic side chains. The first uses a simple single-bead representation, while the second uses a three-bead representation to more accurately represent the planarity of the ring. The one-bead model yields nanorods, while the three-bead model results in nanospheres. The role of different chemical groups in the assembly of nanostructures is identified, along with the importance of steric effects on the packing of the peptides within assemblies.

Multiscale Simulations to Discover Self-Assembled Oligopeptides: A Benchmarking Study

Peptide self-assembly is critical for biomedical and material discovery and production. While it is costly to experimentally test every possible peptide design, computational assessment provides an affordable solution to evaluate many designs and prioritize synthesis and characterization. Following a theoretical investigation, we present a systematic analysis of all-atom and coarse-grained simulations to predict peptide self-assembly. Benchmarking studies of two model dipeptides allow us to assess the impacts of intrinsic properties (such as amino acids and terminal modifications) and external environment (such as salinity) on the simulated aggregation. Further examination of 20 oligopeptides containing two to five amino acids shows good agreement among our theory, simulations, and prior experimental observations. The success rate of our prediction is 90%. Therefore, our theory, simulation, and analysis can be useful to identify peptide designs that can self-assemble and predict the potential nanostructures. These findings lay the ground for future virtual screening of peptide-assembled nanostructures and computer-aided biologics design.

Machine Learning-Guided Adaptive Parametrization for Coupling Terms in a Mixed United-Atom/Coarse-Grained Model for Diphenylalanine Self-Assembly in Aqueous Ionic Liquids

Precise regulation of the peptide self-assembly into ordered nanostructures with intriguing properties has attracted intense attention. However, predicting peptide assembly at atomic resolution is a challenge due to both the structural flexibility of peptides and the associated huge computational costs. A machine learning-guided adaptive parametrization method was proposed for developing a mixed atomic and coarse-grained (CG) model through a multiobjective optimization strategy. Our model incorporates the united-atom (UA) model for diphenylalanine (P) and the polarizable electrostatic-variable coarse-grained (VaCG) model for aqueous ionic liquid [BMIM]+[BF4]- solution. In this mixed model, the coupling van der Waals (vdW) interaction is addressed by introducing virtual sites (VS) in the UA model to interact with solvent CG beads. The coupling parameters, including the electrostatic parameter and vdW parameters, are automatically optimized through ML-guided adaptive parametrization. The performance of this model was tested by some microstructural properties, e.g., the average number of P-P intermolecular hydrogen bonds (HBs) and radius distribution functions (RDFs) between P and different fragments of IL, in comparison with all-atom (AA) simulations. The computational cost is significantly reduced using such a parametrization scheme, which could search tens of thousands of force-field parameter sets, while needing only a small fraction of them to be assessed with molecular dynamics (MD) simulations. We used such a mixed resolution model to investigate the self-assembly in IL-water mixtures with variants of IL concentration (X). The long-range-ordered fibril structure is formed in a pure water system (X = 0). With an increase of IL concentrations, the formation of an ordered self-assembly nanostructure is prohibited, instead forming branched fibril at X = 2 mol % or amorphous aggregates when X > 10 mol %, resulting from the interplay between π-stacking and HB interactions between P and IL. The qualitative agreement between the simulated structures and the observed morphologies in experiments indicates the applicability of ML-guided parametrization strategy in the study of complex systems, such as polymers, lipid bilayers, and polysaccharides.

SARS-CoV-2 external structures interacting with nanospheres using docking and molecular dynamics

Coronavirus is caused by the SARS-CoV-2 virus has shown rapid proliferation and scarcity of treatments with proven effectiveness. In this way, we simulated the hospitalization of carbon nanospheres, with external active sites of the SARS-CoV-2 virus (M-Pro, S-Gly and E-Pro), which can be adsorbed or inactivated when interacting with the nanospheres. The computational procedures performed in this work were developed with the SwissDock server for molecular docking and the GROMACS software for molecular dynamics, making it possible to extract relevant data on affinity energy, distance between molecules, free Gibbs energy and mean square deviation of atomic positions, surface area accessible to solvents. Molecular docking indicates that all ligands have an affinity for the receptor's active sites. The nanospheres interact favorably with all proteins, showing promising results, especially C60, which presented the best affinity energy and RMSD values ​​for all protein macromolecules investigated. The C60 with E-Pro exhibited the highest affinity energy of -9.361 kcal/mol, demonstrating stability in both molecular docking and molecular dynamics simulations. Our RMSD calculations indicated that the nanospheres remained predominantly stable, fluctuating within a range of 2 to 3 Å. Additionally, the analysis of other structures yielded promising results that hold potential for application in other proteases.Communicated by Ramaswamy H. Sarma.

Ion-Induced Reassembly between Protein Nanotubes and Nanospheres

Proteins used as building blocks to template nanostructures with manifold morphologies have been widely reported. Understanding their self-assembly and reassembly mechanism is important for designing functional biomaterials. Herein, we show that enzyme-hydrolyzed α-lactalbumin (α-lac) can self-assemble into either nanotubes in the presence of Ca2+ ions or nanospheres in the absence of Ca2+ in solution. Remarkably, such assembled α-lac nanotubes can be elongated by adding preassembled α-lac nanospheres and Ca2+ solution, which suggests that the self-assembled α-lac nanospheres undergo disassembly and reassembly processes into existing nanotube nuclei. By performing atomic force microscopy (AFM), transmission electron microscopy (TEM), and confocal laser scanning microscopy (CLSM), it indicates that there is an equilibrium among nanotubes, nanospheres, hydrolyzed α-lac, and Ca2+ in solution. The structural transition between nanotubes and nanospheres is driven from a less stable structure into a more stable structure determined by the conditions. During the transition from nanospheres into nanotubes, the hydrolyzed α-lac in nanospheres transfers into helical ribbon form at both nanotube extremities. Then helical ribbons close into mature nanotubes, extending the length of the initial nuclei. Besides, by dilution or adding ethylene glycol bis(2-aminoethyl ether) tetraacetic acid (EGTA), the decreased Ca2+ concentration in solution drives the Ca2+ dissociating from nanotubes into solution, leading to the transitions from nanotubes into nanospheres. The reversible transformation between nanotubes and nanospheres is achieved by adjusting the pH value from 7.5 to 5.0 and back to 7.5. This is because the stability of nanotubes decreases from pH 7.5 to 5 but increases from 5 to 7.5. Significantly, this approach can be used for the fabrication of various responsive nanomaterials from the same starting material.

Computation meets experiment: identification of highly efficient fibrillating peptides

Self-assembling peptides are of huge interest for biological, medical and nanotechnological applications. The enormous chemical variety that is available from the 20 amino acids offers potentially unlimited peptide sequences, but it is currently an issue to predict their supramolecular behavior in a reliable and cheap way. Herein we report a computational method to screen and forecast the aqueous self-assembly propensity of amyloidogenic pentapeptides. This method was found also as an interesting tool to predict peptide crystallinity, which may be of interest for the development of peptide based drugs.

Influence of pH on the self-assembly of diphenylalanine peptides: molecular insights from coarse-grained simulations

Nanostructures fabricated from peptide self-assemblies are attracting increasing attention owing to their possible applications in biology and nanotechnology. A known example is an aromatic dipeptide (diphenylalanine, FF) which is extracted from Alzheimer's β-amyloid polypeptide as the core recognition motif for molecular self-assembly. Many studies have been carried out to organize FF peptides into various functional ordered nanostructures. For potential applications of self-assembled FF-based nanomaterials, it becomes important to consider some influencing factors (e.g., solvents, peptide concentrations, pH, temperature, etc.) on the self-assembly process. Among these factors, the effect of pH on the self-assembly process of FF peptides into assembled nanostructures through simulation studies is the main focus of the present work. In the current study, we have investigated the assembly pathway of 1000 FF peptides and qualitatively evaluated the morphological changes of FF-based nanostructures at different pH values by performing extensive coarse-grained molecular dynamics (CG-MD) simulations. Structural analyses suggest that FF peptides can spontaneously assemble into nanotubes with different shapes under acidic, neutral and basic conditions. Based on the analysis of FF nanostructure formation pathways in different pH solutions, the self-assembly of the nanotube involves the aggregation of molecules to form a bilayer, the curling of a bilayer to form a vesicle and the transformation of a vesicle into a tubular structure. It is noted that a flat hollow columnar structure is observed as a special intermediate state during the transformation process of a vesicle-like to a tube-like structure. Energetic analysis suggests that the aggregation of FF peptides is driven by the vdW interactions but the aggregation shape is mainly affected by the electrostatic interactions. Overall, this study provides further understanding of the self-assembly behavior of aromatic short peptide derivatives in different pH solutions.

A Facile and Versatile Approach to Construct Photoactivated Peptide Hydrogels by Regulating Electrostatic Repulsion

Short peptides that can respond to external stimuli have been considered as the preferred building blocks to construct hydrogels for biomedical applications. In particular, photoresponsive peptides that are capable of triggering the formation of hydrogels upon light irradiation allow the properties of hydrogels to be changed remotely by precise and localized actuation. Here, we used the photochemical reaction of the 2-nitrobenzyl ester group (NB) to develop a facile and versatile strategy for constructing photoactivated peptide hydrogels. The peptides with high aggregation propensity were designed as hydrogelators, which were photocaged by a positively charged dipeptide (KK) to provide strong charge repulsion and prevent self-assembly in water. Light irradiation led to the removal of KK and triggered the self-assembly of peptides and the formation of hydrogel. Light stimulation endows spatial and temporal control, which enables the formation of hydrogel with precisely tunable structure and mechanical properties. Cell culture and behavior study indicated that the optimized photoactivated hydrogel was suitable for 2D and 3D cell culture, and its photocontrollable mechanical strength could regulate the spreading of stem cells on its surface. Therefore, our strategy provides an alternative way to construct photoactivated peptide hydrogels with wide applications in biomedical areas.

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.

Metal-Ion-Induced Evolution of Phenylalanine Self-Assembly: Structural Polymorphism of Novel Metastable Intermediates

The self-assembly of aromatic amino acids has been widely studied due to their ability to form well-defined amyloid-like fibrillar structures. Herein, for the first time, we report the existence of different metastable intermediate states of diverse morphologies, for example, droplets, spheres, vesicles, flowers, and toroids, that are sequentially formed in aqueous medium during the self-assembly process of phenylalanine in the presence of different divalent (Zn²⁺, Cd²⁺, and Hg²⁺) and trivalent (Al³⁺, Ga³⁺, and In³⁺) metal ions having low pK_a values. Due to metal ion-amino acid coordination and strong hydrophobic interaction induced by these metal ions, spherical aggregates are obtained at the initial stage of the structural evolution and further transformed into other intermediate states. Our work may facilitate understanding of the role of metal ions in the amino acid self-assembly process and broaden future applications of the obtained nanostructures in drug delivery, tissue engineering, bioimaging, biocatalysis, and other fields.

Self-assembly pathways in a triphenylalanine peptide capped with aromatic groups

Peptide derivatives and, most specifically, their self-assembled supramolecular structures are being considered in the design of novel biofunctional materials. Although the self-assembly of triphenylalanine homopeptides has been found to be more versatile than that of homopeptides containing an even number of residues (i.e. diphenylalanine and tetraphenylalanine), only uncapped triphenylalanine (FFF) and a highly aromatic analog blocked at both the N- and C-termini with fluorenyl-containing groups (Fmoc-FFF-OFm), have been deeply studied before. In this work, we have examined the self-assembly of a triphenylalanine derivative bearing 9-fluorenylmethyloxycarbonyl and benzyl ester end-capping groups at the N- and C-termini, respectively (Fmoc-FFF-OBzl). The antiparallel arrangement clearly dominates in β-sheets formed by Fmoc-FFF-OBzl, whereas the parallel and antiparallel dispositions are almost isoenergetic in Fmoc-FFF-OFm β-sheets and the parallel one is slightly favored for FFF. The effects of both the peptide concentration and the medium on the self-assembly process have been examined considering Fmoc-FFF-OBzl solutions in a wide variety of solvent:co-solvent mixtures. In addition, Fmoc-FFF-OBzl supramolecular structures have been compared to those obtained for FFF and Fmoc-FFF-OFm under identical experimental conditions. The strength of π-π stacking interactions involving the end-capping groups plays a crucial role in the nucleation and growth of supramolecular structures, which determines the resulting morphology. Finally, the influence of a non-invasive external stimulus, ultrasounds, on the nucleation and growth of supramolecular structures has been examined. Overall, FFF-based peptides provide a wide range of supramolecular structures that can be of interest in the biotechnological field.

Biochemical Interactions through Microscopic Techniques: Structural and Molecular Characterization

Many researchers and scientists have contributed significantly to provide structural and molecular characterizations of biochemical interactions using microscopic techniques in the recent decade, as these biochemical interactions play a crucial role in the production of diverse biomaterials and the organization of biological systems. The properties, activities, and functionalities of the biomaterials and biological systems need to be identified and modified for different purposes in both the material and life sciences. The present study aimed to review the advantages and disadvantages of three main branches of microscopy techniques (optical microscopy, electron microscopy, and scanning probe microscopy) developed for the characterization of these interactions. First, we explain the basic concepts of microscopy and then the breadth of their applicability to different fields of research. This work could be useful for future research works on biochemical self-assembly, biochemical aggregation and localization, biological functionalities, cell viability, live-cell imaging, material stability, and membrane permeability, among others. This understanding is of high importance in rapid, inexpensive, and accurate analysis of biochemical interactions.

Structural Properties of Phenylalanine-Based Dimers Revealed Using IR Action Spectroscopy

Peptide segments with phenylalanine residues are commonly found in proteins that are related to neurodegenerative diseases. However, the self-assembly of phenylalanine-based peptides can be also functional. Peptides containing phenylalanine residues with different side caps, composition, and chemical alteration can form different types of nanostructures that find many applications in technology and medicine. Various studies have been performed in order to explain the remarkable stability of the resulting nanostructures. Here, we study the early stages of self-assembly of two phenylalanine derived peptides in the gas phase using IR action spectroscopy. Our focus lies on the identification of the key intra- and intermolecular interactions that govern the formation of the dimers. The far-IR region allowed us to distinguish between structural families and to assign the 2-(2-amino-2-phenylacetamido)-2-phenylacetic acid (PhgPhg) dimer to a very symmetric structure with two intermolecular hydrogen bonds and its aromatic rings folded away from the backbone. By comparison with the phenylalanine-based peptide cyclic L-phenylalanyl-L-phenylalanine (cyclo-FF), we found that the linear FF dimer likely adopts a less ordered structure. However, when one more phenylalanine residue is added (FFF), a more structurally organized dimer is formed with several intermolecular hydrogen bonds.

A crystal-structural study of Pauling-Corey rippled sheets

Following the seminal theoretical work on the pleated β-sheet published by Pauling and Corey in 1951, the rippled β-sheet was hypothesized by the same authors in 1953. In the pleated β-sheet the interacting β-strands have the same chirality, whereas in the rippled β-sheet the interacting β-strands are mirror-images. Unlike with the pleated β-sheet that is now common textbook knowledge, the rippled β-sheet has been much slower to evolve. Much of the experimental work on rippled sheets came from groups that study aggregating racemic peptide systems over the course of the past decade. This includes MAX1/DMAX hydrogels (Schneider), L/D-KFE8 aggregating systems (Nilsson), and racemic Amyloid β mixtures (Raskatov). Whether a racemic peptide mixture is “ripple-genic” (i.e., whether it forms a rippled sheet) or “pleat-genic” (i.e., whether it forms a pleated sheet) is likely governed by a complex interplay of thermodynamic and kinetic effects. Structural insights into rippled sheets remain limited to only a very few studies that combined sparse experimental structural constraints with molecular modeling. Crystal structures of rippled sheets are needed so we can rationally design rippled sheet architectures. Here we report a high-resolution crystal structure, in which (l,l,l)-triphenylalanine and (d,d,d)-triphenylalanine form dimeric antiparallel rippled sheets, which pack into herringbone layer structures. The arrangements of the tripeptides and their mirror-images in the individual dimers were in excellent agreement with the theoretical predictions by Pauling and Corey. A subsequent mining of the PDB identified three orphaned rippled sheets among racemic protein crystal structures.

Following the seminal theoretical work on the pleated β-sheet published by Pauling and Corey in 1951, the rippled β-sheet was hypothesized by the same authors in 1953.

Computational and Experimental Protocols to Study Cyclo-dihistidine Self- and Co-assembly: Minimalistic Bio-assemblies with Enhanced Fluorescence and Drug Encapsulation Properties

Our published studies on the self- and co-assembly of cyclo-HH peptides demonstrated their capacity to coordinate with Zn(II), their enhanced photoluminescence and their ability to self-encapsulate epirubicin, a chemotherapy drug. Here, we provide a detailed description of computational and experimental methodology for the study of cyclo-HH self- and co-assembling mechanisms, photoluminescence, and drug encapsulation properties. We outline the experimental protocols, which involve fluorescence spectroscopy, transmission electron microscopy, and atomic force microscopy protocols, as well as the computational protocols, which involve structural and energetic analysis of the assembled nanostructures. We suggest that the computational and experimental methods presented here can be generalizable, and thus can be applied in the investigation of self- and co-assembly systems involving other short peptides, encapsulating compounds and binding to ions, beyond the particular ones presented here.

A hybrid coarse-grained model for structure, solvation and assembly of lipid-like peptides

Reconstituted photosynthetic proteins which are activated upon exposure to solar energy hold enormous potential for powering future solid state devices and solar cells. The functionality and integration of these proteins into such devices has been successfully enabled by lipid-like peptides. Yet, a fundamental understanding of the organization of these peptides with respect to the photosynthetic proteins and themselves remains unknown and is critical for guiding the design of such light-activated devices. This study investigates the relative organization of one such peptide sequence V₆K₂ (V: valine and K: lysine) within assemblies. Given the expansive spatiotemporal scales associated with this study, a hybrid coarse-grained (CG) model which captures the structure, conformation and aggregation of the peptide is adopted. The CG model uses a combination of iterative Boltzmann inversion and force matching to provide insight into the relative organization of V₆K₂ in assemblies. The CG model reproduces the structure of a V₆K₂ peptide sequence along with its all atom (AA) solvation structure. The relative organization of multiple peptides in an assembly, as captured by CG simulations, is in agreement with corresponding results from AA simulations. Also, a backmapping procedure reintroduces the AA details of the peptides within the aggregates captured by the CG model to demonstrate the relative organization of the peptides. Furthermore, a large number of peptides self-assemble into an elongated micelle in the CG simulation, which is consistent with experimental findings. The coarse-graining procedure is tested for transferability to longer peptide sequences, and hence can be extended to other amphiphilic peptide sequences.

Expanding the Structural Diversity and Functional Scope of Diphenylalanine-Based Peptide Architectures by Hierarchical Coassembly

Modulation of the structural diversity of diphenylalanine-based assemblies by molecular modification and solvent alteration has been extensively explored for bio- and nanotechnology. However, regulation of the structural transition of assemblies based on this minimal building block into tunable supramolecular nanostructures and further construction of smart supramolecular materials with multiple responsiveness are still an unmet need. Coassembly, the tactic employed by natural systems to expand the architectural space, has been rarely explored. Herein, we present a coassembly approach to investigate the morphology manipulation of assemblies formed by N-terminally capped diphenylalanine by mixing with various bipyridine derivatives through intermolecular hydrogen bonding. The coassembly-induced structural diversity is fully studied by a set of biophysical techniques and computational simulations. Moreover, multiple-responsive two-component supramolecular gels are constructed through the incorporation of functional bipyridine molecules into the coassemblies. This study not only depicts the coassembly strategy to manipulate the hierarchical nanoarchitecture and morphology transition of diphenylalanine-based assemblies by supramolecular interactions but also promotes the rational design and development of smart hydrogel-based biomaterials responsive to various external stimuli.

Replica Exchange Molecular Dynamics of Diphenylalanine Amyloid Peptides in Electric Fields

The self-assembling propensity of amyloid peptides such as diphenylalanine (FF) allows them to form ordered, nanoscale structures, with biocompatible properties important for biomedical applications. Moreover, piezoelectric properties allow FF molecules and their aggregates (e.g., FF nanotubes) to be aligned in a controlled way by the application of external electric fields. However, while the behavior of FF nanostructures emerges from the biophysical properties of the monomers, the detailed responses of individual peptides to both temperature and electric fields are not fully understood. Here, we study the temperature-dependent conformational dynamics of FF peptides solvated in explicit water molecules, an environment relevant to biomedical applications, by using an enhanced sampling method, replica exchange molecular dynamics (REMD), in conjunction with applied electric fields. Our simulations highlight and overcome possible artifacts that may occur during the setup of REMD simulations of explicitly solvated peptides in the presence of external electric fields, a problem particularly important in the case of short peptides such as FF. The presence of the external fields could overstabilize certain conformational states in one or more REMD replicas, leading to distortions of the underlying potential energy distributions observed at each temperature. This can be overcome by correcting the REMD initial conditions to include the lower-energy conformations induced by the external field. We show that the converged REMD data can be analyzed using a Markovian description of conformational states and show that a rather complex, 3-state, temperature-dependent conformational dynamics in the absence of electric fields collapses to only one of these states in the presence of the electric fields. These details on the temperature- and electric-field-dependent thermodynamic and kinetic properties of small FF amyloid peptides can be useful in understanding and devising new methods to control their aggregation-prone biophysical properties and, possibly, the structural and biophysical properties of FF molecular nanostructures.

Bolaamphiphilic Bis-Dehydropeptide Hydrogels as Potential Drug Release Systems

The self-assembly of nanometric structures from molecular building blocks is an effective way to make new functional materials for biological and technological applications. In this work, four symmetrical bolaamphiphiles based on dehydrodipeptides (phenylalanyldehydrophenylalanine and tyrosyldehydrophenylalanine) linked through phenyl or naphthyl linkers (terephthalic acid and 2,6-naphthalenedicarboxylic acid) were prepared, and their self-assembly properties were studied. The results showed that all compounds, with the exception of the bolaamphiphile of tyrosyldehydrophenylalanine and 2,6-naphthalene dicarboxylic acid, gave self-standing hydrogels with critical gelation concentrations of 0.3 wt % and 0.4 wt %, using a pH trigger. The self-assembly of these hydrogelators was investigated using STEM microscopy, which revealed a network of entangled fibers. According to rheology, the dehydrodipeptide bolaamphiphilic hydrogelators are viscoelastic materials with an elastic modulus G′ that falls in the range of native tissue (0.37 kPa brain–4.5 kPa cartilage). In viability and proliferation studies, it was found that these compounds were non-toxic toward the human keratinocyte cell line, HaCaT. In sustained release assays, we studied the effects of the charge present on model drug compounds on the rate of cargo release from the hydrogel networks. Methylene blue (MB), methyl orange (MO), and ciprofloxacin were chosen as cationic, anionic, and overall neutral cargo, respectively. These studies have shown that the hydrogels provide a sustained release of methyl orange and ciprofloxacin, while methylene blue is retained by the hydrogel network.

Disassembly and reassembly of diphenylalanine crystals through evaporation of solvent

HYPOTHESIS

Crystalline self-assemblies of diphenylalanine (FF) are since long back considered to be related to Alzheimer's disease. An improved understanding of the mechanism behind the formation of such structures can lead to strategies for investigating the dynamic processes of assembly and disassembly of FF.

EXPERIMENT

The assembly, disassembly and reassembly of FF crystals are influenced by the solvent composition and can be triggered by evaporation of solvent. In this work these processes are directly monitored, and the structures obtained are analyzed.

FINDINGS

The role of the solvent for assembly, disassembly and reassembly of diphenylalanine crystals has been demonstrated. The initial crystal structure formed via self-assembly of FF monomers can be transformed into needle-like crystals and further to hollow hexagonal microtubes through evaporation of the solvent. It is shown that all the assembly-disassembly processes are spontaneous and driven by thermodynamics. It is also found that some of the crystalline structures exhibit optical waveguiding properties.

Targeted drug delivery strategies for precision medicines

Progress in the field of precision medicine has changed the landscape of cancer therapy. Precision medicine is propelled by technologies that enable molecular profiling, genomic analysis, and optimized drug design to tailor treatments for individual patients. Although precision medicines have resulted in some clinical successes, the use of many potential therapeutics has been hindered by pharmacological issues, including toxicities and drug resistance. Drug delivery materials and approaches have now advanced to a point where they can enable the modulation of a drug's pharmacological parameters without compromising the desired effect on molecular targets. Specifically, they can modulate a drug's pharmacokinetics, stability, absorption, and exposure to tumours and healthy tissues, and facilitate the administration of synergistic drug combinations. This Review highlights recent progress in precision therapeutics and drug delivery, and identifies opportunities for strategies to improve the therapeutic index of cancer drugs, and consequently, clinical outcomes.

Nano-assemblies with core-forming hydrophobic polypeptide via polymerization-induced self-assembly (PISA)

The aim of this study is to produce self-assembled structures with hydrophobic polypeptide cores via Reversible Addition–Fragmentation chain Transfer (RAFT) – mediated Polymerisation-Induced Self-Assembly (PISA).

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.

Revealing Thermodynamics and Kinetics of Lipid Self-Assembly by Markov State Model Analysis

Self-assembly is ubiquitous in the realm of biology and has become an elegant bottom-up approach to fabricate new materials. Although molecular dynamics (MD) simulations can complement experiments by providing the missing atomic details, it still remains a grand challenge to reveal the thermodynamic and kinetic information on a self-assembly system. In this work, we demonstrate for the first time that the Markov state model analysis can be used to delineate the variation of free energy during the self-assembly process of a typical amphiphilic lipid dipalmitoyl-phosphatidylcholine (DPPC). Free energy profiles against the solvent-accessible surface area and the root-mean-square deviation have been derived from extensive MD results of more than five hundred trajectories, which identified a metastable crossing-cylinder (CC) state and a transition state of the distorted bilayer with a free energy barrier of ∼0.02 kJ mol^-1 per DPPC lipid, clarifying a long-standing speculation for 20 years that there exists a free energy barrier during lipid self-assembly. Our simulations also unearth two mesophase structures at the early stage of self-assembly, discovering two assembling pathways to the CC state that have never been reported before. Further thermodynamic analysis derives the contributions from the enthalpy and the entropy terms to the free energy, demonstrating the critical role played by the enthalpy-entropy compensation. Our strategy opens the door to quantitatively understand the self-assembly processes in general and provides new opportunities for identifying common thermodynamic and kinetic patterns in different self-assembly systems and inspiring new ideas for experiments. It may also contribute to the refinement of force field parameters of various self-assembly systems.

Role of alkylated residues in the tetrapeptide self-assembly-A molecular dynamics study

Designing peptide sequences that self-assemble into well-defined nanostructures can open a new venue for the development of novel drug carriers and molecular contrast agents. Current approaches are often based on a linear block-design of amphiphilic peptides where a hydrophilic peptide chain is terminated by a hydrophobic tail. Here, a new template for a self-assembling tetrapeptide (YXKX, Y = tyrosine, X = alkylated tyrosine, K = lysine) is proposed with two distinct sides relative to the peptide's backbone: alkylated hydrophobic residues on one side and hydrophilic residues on the other side. Using all-atom molecular dynamics simulations, the self-assembly pathway of the tetrapeptide is analyzed for two different concentrations. At both concentrations, tetrapeptides self-assembled into a nanosphere structure. The alkylated tyrosines initialize the self-assembly process via a strong hydrophobic effect and to reduce exposure to the aqueous solvent, they formed a hydrophobic core. The hydrophilic residues occupied the surface of the self-assembled nanosphere. Ordered arrangement of tetrapeptides within the nanosphere with the backbone hydrogen bonding led to a beta sheet formation. Alkyl chain length constrained the size and shape of the nanosphere. This study provides foundation for further exploration of self-assembling structures that are based on peptides with hydrophobic and hydrophilic moieties located on the opposite sides of a peptide backbone.

Recent advances in the fabrication, functionalization, and bioapplications of peptide hydrogels

Self-assembled peptide-based nanomaterials have exhibited wide application potential in the fields of materials science, nanodevices, biomedicine, tissue engineering, biosensors, energy storage, environmental science, and others. Due to their porous structure, strong mechanical stability, high biocompatibility, and easy functionalization, three-dimensional self-assembled peptide hydrogels revealed promising potential in bio-related applications. To present the advances in this interesting topic, we present a review on the synthesis and functionalization of peptide hydrogels, as well as their applications in drug delivery, antibacterial materials, cell culture, biomineralization, bone tissue engineering, and biosensors. Specifically, we focus on the fabrication methods of peptide hydrogels through physical, chemical, and biological stimulations. In addition, the functional design of peptide hydrogels by incorporation with polymers, DNA, protein, nanoparticles, and carbon materials is introduced and discussed in detail. It is expected that this work will be helpful not only for the design and synthesis of various peptide-based nanostructures and nanomaterials, but also for the structural and functional tailoring of peptide-based nanomaterials to meet specific demands.

Introduction to peptide soft materials

Arindam Banerjee and Ian W. Hamley introduce the Soft Matter themed collection on peptide soft materials.

Peptide-based vesicles and droplets: a review

Peptide assembly is an increasingly important field of study due to the versatility, tunability and vast design space of amino acid based biomolecular assemblies. Peptides can be precisely engineered to possess various useful properties such as the ability to form supramolecular assemblies, desired response to pH, or thermal stability. These peptide supramolecular assemblies have diverse morphologies including vesicles, nanotubes, nanorods and ribbons. Of specific interest is the domain of engineering peptides that aggregate into spherical nanostructures due to their encapsulation properties: the ability to hold, transport and release chemical payloads in a controllable manner. This is invaluable to the fields of nanomedicine and targeted drug delivery. In this review, the state of the art in the domain of peptide-based vesicles and nanospheres is summarized. Specifically, an overview of the assembly of peptides into nanovesicles and nanospheres is provided. Both aromatic as well as aliphatic side chain amino acids are discussed. The domain of aromatic side chained amino acid residues is largely dominated by phenylalanine based peptides and variants thereof. Tyrosine also demonstrates similar aggregation properties. Both experimentally and computationally driven approaches are discussed. The domain of aliphatic amino acid residues based vesicles and droplets is broader, and details multiple amino acid residues such as alanine, valine, lysine, glycine, proline, and aspartic acid. Finally, a discussion on potential future directions is provided.

Constitutionally Isomeric Aromatic Tripeptides: Self-Assembly and Metal-Ion-Modulated Transformations

Self-assembling peptides based on aromatic amino acids can adopt diverse nanostructures which primarily depend on their molecular structures. Therefore, to understand the nature of self-assembly on the molecular level we rationally designed two constitutional isomers of short aromatic peptides. The first isomer consists of a tyrosine moiety at the N-terminus and the second isomer consists of a tyrosine moiety at the C-terminus of the FF peptide, a core recognition motif of Amyloid β peptides. Therefore, it can be considered that both the designed tripeptides are the analogues of the FFF peptide with only atomic(-H) level replacement by -OH functional group on the first and last phenyl ring, respectively. The first isomer self-assembled into 2D porous nanosheets ("Nanowebs"), however the second isomers produced toroidal shapes with central spheres ("Nano-Saturn" like assemblies). Interestingly, the presence of the transition-metal ions (copper, zinc and iron) triggered the self-assembly of both the peptides into fibrous circular discs, nanomats and nanoplates like assembly.

Solid-state synthesis of cyclo LD-diphenylalanine: A chiral phase built from achiral subunits

The solid-state structure of LL/DD or LD/DL diphenylalanine diluted in KBr pellets is studied by infrared (IR) absorption and vibrational circular dichroism (VCD) spectroscopy. The structure depends on the absolute configuration of the residues. The natural LL diphenylalanine exists as a mixture of neutral and zwitterionic structures, depending on the humidity of the sample, while mostly the zwitterion is observed for LD diphenylalanine whatever the experimental conditions. The system undergoes spontaneous cyclization upon heating at 125°C, resulting to the formation of a diketopiperazine (DKP) dipeptide as the only product. The reaction is faster for LD than for LL diphenylalanine. As expected, LL and DD diphenylalanine react to form the LL and DD enantiomers of cyclo diphenylalanine. Interestingly, the DKP dipeptides formed from the LD or DL diphenylalanine show unexpected optical activity, with opposite VCD spectra for the products formed from the LD and DL reagents. This is explained in terms of chirality synchronization between the monomers within the crystal, which retain the symmetry of the reagent, resulting to the formation of a new chiral phase made from transiently chiral molecules.

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.

A Comprehensive Study on Self-Assembly and Gelation of C13-Dipeptides-From Design Strategies to Functionalities

Computational and experimental methods were applied to investigate the self-assembly and gelation of C₁₃-dipeptides. A modified aggregation propensity (AP_S) was introduced to correlate the effects of side chains of amino acids on the tendency to aggregate. From the experimental results, the ranges of 0.156 < AP_S < 0.250 seemed to be a proper region for the C₁₃-dipeptides to form hydrogels, while other molecules with higher or lower AP_S were insoluble or dissociated. As observed from molecular dynamics simulations, the C₁₃-dipeptides first formed small aggregates through hydrophobic interactions and then rearranged through electrostatic attractions and hydrogen bonds for self-assembly. The C₁₃-dipeptides tended to be antiparallel packed, as shown by hydrogen bonding analyses. Experimental observations and analyses on the structures of C₁₃-dipeptide hydrogels matched the computational conclusions very well. From the five selected gelators, i.e., C₁₃-GW, C₁₃-VY, and C₁₃-WT, strong π-π stacking was observed. For C₁₃-WS, strong hydrogen bonding was found, and in C₁₃-WY, both strong π-π interactions and hydrogen bonds were found. It takes around 90 min or longer for C₁₃-dipeptides to form hydrogels, and those formed by C₁₃-WY and C₁₃-WS had weak water holding capacities, which might be due to strong intermolecular hydrogen bonding. From rheological studies, the C₁₃-dipeptides formed strong chemical gels that were stabilized by strong interactions between the molecular aggregates. These gelators exhibit the potentials to be environmentally friendly substitutes for the common functionalized peptide gelators.

The molecular mechanism of robust macrophage immune responses induced by PEGylated molybdenum disulfide

Molybdenum disulfide (MoS2), a representative hexagonal transition metal dichalcogenide (TMD), has been extensively exploited in biomedical applications due to its unique physicochemical properties and biocompatibility. However, the lack of adequate data regarding how MoS2 activates immunological responses of macrophages remains a key concern for its risk assessment. Here, we employ a combined theoretical and experimental approach to investigate the interactions of MoS2 and PEGylated MoS2 (MoS2-PEG) with macrophages. We first perform molecular dynamics simulations to examine the atomic-detailed interactions of MoS2 and MoS2-PEG nanoflakes with a realistic model of the macrophage membrane. We show that a small MoS2 nanoflake (edge length of 2.86 nm) is capable of penetrating the macrophage membrane independent of its concentration. We also demonstrate that when initiated with a corner point-on configuration, the surface-bound PEG chains of MoS2-PEG hinder its membrane insertion process, leading to a prolonged passage through the membrane. Moreover, when placed in a face-on arrangement initially, the MoS2-PEG exhibits a lower binding free energy than pristine MoS2 after its adsorption on the membrane surface. The PEG chains can even insert and get buried in the outer leaflet of the membrane, providing additional contact for membrane adsorption. Our flow cytometric experiments then show that the responses of macrophages to either MoS2-PEG or MoS2 are significantly higher than that of the control (no nanomaterial stimulus), with MoS2-PEG eliciting stronger cytokine secretion than the pristine MoS2. The characteristics of slower/prolonged membrane penetration and stronger membrane adsorption of MoS2-PEG compared to pristine MoS2 explain why it triggers more sustained stimulation and higher cytokine secretion in macrophages as observed in our experiments. Our findings reveal the underlying molecular mechanism of how MoS2-PEG influences the immune responses and suggest its potential applications in nanomedicine involving immune stimulation.

Different platinum crystal surfaces show very distinct protein denaturation capabilities

Different platinum (Pt) surfaces of nanocrystals usually exhibit significant distinctions with regard to various biological, physical, and chemical characteristics, such as bio-recognition, surface wetting, and catalytic activities. In this study, we report for the first time that two shape-controlled Pt nanocrystals with the most common low-index surfaces, Pt(100) and Pt(111), show very dissimilar protein denaturation capabilities based on all-atom molecular dynamics simulations employing the widely used model protein, villin headpiece (HP35). We demonstrate that HP35 is well preserved on the Pt(100) crystal surface, whereas it is severely disrupted on the Pt(111) crystal surface. This surprising difference originates from the distinct water behavior in the first solvation shell (FSS) of the two Pt crystal surfaces. Within the FSS of the Pt(100) crystal surface, water molecules form a very compact and stable monolayer through a highly uniform rhombic hydrogen-bond network. This water monolayer prefers the adsorption of acidic residues (such as Glu and Asp) and acts as a shield to prevent other residues from directly coming into contact with the metal surface. On the other hand, the hydrogen bond network in the water monolayer in the FSS of the Pt(111) crystal surface is very sparse and quite defective, which makes it more vulnerable to the penetration of various residues, particularly those with planar side chains such as Phe, Trp and Arg due to strong dispersion interactions, leading to subsequent protein unfolding. The binding free energy calculations for some key amino acids on the two different crystal surfaces further uncover the molecular origin behind their distinct protein denaturation capability. Our study reveals the vital importance of interfacial water in determining the structure of proteins when binding to different metal crystal surfaces. The discovered molecular mechanisms may be helpful for the future development of a bio-assisted programmable synthetic strategy of sophisticated Pt nanostructures for biomedical applications.

Lanosterol Disrupts the Aggregation of Amyloid-β Peptides

Lanosterol, an amphipathic molecule, was discovered only very recently to effectively hinder the aggregation of lens proteins and dissolve the extremely stable fibrillar aggregates in cataracts. Here, we combined computational and experimental approaches to study how lanosterol disrupts the aggregation of another important peptide, amyloid-β (Aβ) peptide, associated with the Alzheimer's Disease (AD). Molecular dynamics simulations using the core amyloidogenic segment (KLVFFA) of Aβ peptide revealed that lanosterol exhibits at least two types of inhibition mechanism on the self-assembly of Aβ peptides. First, lanosterol entangles with peptides and forms a hydrophobic core with residues Phe-19 and Phe-20 in particular. Second, it interferes with the steric zipper interaction at the β-sheet-β-sheet interface. These simulation data suggest that lanosterol induces the unfolding of the Aβ peptide and the separation of the β-sheet layers. This predicted inhibition effect of lanosterol was then confirmed by an in vitro ThT fluorescence assay and AFM imaging. The cell toxicity assay also showed that the treatment of lanosterol indeed mitigates the cytotoxicity of the Aβ peptide in PC-12 cells. Moreover, lanosterol shows a stronger suppression effect on Aβ peptides' aggregation than cholesterol because of its higher hydrophobicity. This result establishes a foundation for the development of lanosterol-based potential therapies for AD and other protein conformational diseases.

Parameterization of Molybdenum Disulfide Interacting with Water Using the Free Energy Perturbation Method

Water contact angles (WCA) are often used to parametrize force field parameters of novel 2D nanomaterials, such as molybdenum disulfide (MoS₂), which has emerged as a promising nanomaterial in many biomedical applications due to its unique and impressive properties. However, there is a wide range of water-MoS₂ contact angles in the literature depending on the aging process on the surface of a MoS₂ nanosheet and/or substrate material. In this study, we revisit and optimize existing parameters for the basal plane of MoS₂ with two popular water models, TIP3P and SPC/E, using the wide range of WCAs from various experiments. We develop and deploy the free energy perturbation method for parametrizing MoS₂ with experimentally determined WCAs for both fresh and aged surfaces. Energy decomposition analysis on the simulation trajectories reveals that MoS₂-water interaction is dominated by van der Waals interaction, which mainly comes from the top layer of MoS₂. We conclude that to describe both fresh and aged MoS₂ surfaces it is convenient to only adjust the Lennard-Jones parameter ε_S (the depth of the potential well of a sulfur atom), which displays a surprisingly linear correlation with WCAs.

Aggregation kinetics of short peptides: All-atom and coarse-grained molecular dynamics study

Peptides can aggregate into ordered structures with different morphologies. The aggregation mechanism and evolving structures are the subject of intense research. In this paper we have used molecular dynamics to examine the sequence-dependence of aggregation kinetics for three short peptides: octaalanine (Ala8), octaasparagine (Asn8), and the heptapeptide GNNQQNY (abbreviated as GNN). First, we compared the aggregation of 20 randomly distributed peptides using the coarse-grained MARTINI force field and the atomistic OPLS-AA force field. We found that the MARTINI and OPLS-AA aggregation kinetics are similar for Ala8, Asn8, and GNN. Second, we used the MARTINI force field to study the early stages of aggregation kinetics for a larger system with 72 peptides. In the initial stage of aggregation small clusters grow by monomer addition. In the second stage, when the free monomers are depleted, the dominant cluster growth path is cluster-cluster coalescence. We quantified the aggregation kinetics in terms of rate equations. Our study shows that the initial aggregation kinetics are similar for Ala8, Asn8, and GNN but the molecular details can be different, especially for MARTINI Ala8. We hypothesize that peptide aggregation proceed in two steps. In the first step amorphous aggregates are formed, and then, in the second step, they reorganize into ordered structures. We conclude that sequence-specific differences show up in the second step of aggregation.

Aryl-viologen pentapeptide self-assembled conductive nanofibers

A pentapeptide sequence was functionalized with an asymmetric arylated methyl-viologen (AVI3D2) and through controllable β-sheet self-assembly, conductive nanofibers were formed. Using a combination of spectroscopic techniques and conductive atomic force microscopy, we investigated the molecular conformation of the resultant AVI3D2 fibers and how their conductivity is affected by β-sheet self-assembly. These conductive nanofibers have potential for future exploration as molecular wires in optoelectronic applications.

Conformation Dependence of Diphenylalanine Self-Assembly Structures and Dynamics: Insights from Hybrid-Resolution Simulations

The molecular design of peptide-assembled nanostructures relies on extensive knowledge pertaining to the relationship between conformational features of peptide constituents and their behavior regarding self-assembly, and characterizing the conformational details of peptides during their self-assembly is experimentally challenging. Here, we demonstrate that a hybrid-resolution modeling method can be employed to investigate the role that conformation plays during the assembly of terminally capped diphenylalanines (FF) through microsecond simulations of hundreds or thousands of peptides. Our simulations discovered tubular or vesicular nanostructures that were consistent with experimental observation while reproducing critical self-assembly concentration and secondary structure contents in the assemblies that were measured in our experiments. The atomic details provided by our method allowed us to uncover diverse FF conformations and conformation dependence of assembled nanostructures. We found that the assembled morphologies and the molecular packing of FFs in the observed assemblies are linked closely with side-chain angle and peptide bond orientation, respectively. Of various conformations accessible to soluble FFs, only a select few are compatible with the assembled morphologies in water. A conformation resembling a FF crystal, in particular, became predominant due to its ability to permit highly ordered and energetically favorable FF packing in aqueous assemblies. Strikingly, several conformations incompatible with the assemblies arose transiently as intermediates, facilitating key steps of the assembly process. The molecular rationale behind the role of these intermediate conformations were further explained. Collectively, the structural details reported here advance the understanding of the FF self-assembly mechanism, and our method shows promise for studying peptide-assembled nanostructures and their rational design.

Self-Assembly of Amphiphilic Peptides for Recognizing High Furin-Expressing Cancer Cells

Self-assembled nanostructures of amphiphilic peptides have a wide range of applications in bioimaging and delivery systems. In this study, we design and synthesize a biocompatible amphiphilic peptide (C-3) consisting of an RVRRFFF sequence and a nitrobenzoxadiazole fluorophore that can self-assemble into stable micelles for specifically detecting furin, a kind of proprotein convertase with promoting tumor progression. The self-assembly of C-3 with a β-sheet nanostructure is capable of a rapid and specific response to furin in only 5 min in aqueous solution because of the existence of the RVRR motif in the C-3 molecule. The C-3 nanostructures thus can selectively distinguish high furin-expressing cancer cells, like MDA-MB-231 cells, a kind of human breast cancer cells, from normal cells. Furthermore, the C-3 self-assembly can stay in living cells for a long time and are capable of durable detection of intracellular furin, being good for tracer analysis. To our knowledge, this is the first example of self-assembly of a soluble amphiphilic peptide that can selectively detect furin in high furin-expressing live cells.

Applications of self-assembling ultrashort peptides in bionanotechnology

Peptides are intriguing building blocks for a variety of applications in bionanotechnology. Peptides can self-assemble into well-ordered nanostructures. Among the various nanomorphology forms, peptide nanofibers and nanotubes are relevant in biomedical applications. In this review, their applications as tissue engineering scaffolds, drug delivery vehicles, three-dimensional printing bioinks and bioimaging nanoprobes will be illustrated. This review article describes di-, tri-, tetra-peptides because they are cost-effective, simple to prepare, and amenable to production on a large scale.

Ultrashort peptide applications in bionanotechnology.