Sequence-Dependent Structural Stability of Self-Assembled Cylindrical Nanofibers by Peptide Amphiphiles

Impact of Peptide Sequences on Their Structure and Function: Mimicking of Virus-Like Nanoparticles for Nucleic Acid Delivery

We rationally designed a series of amphiphilic hepta-peptides enriched with a chemically conjugated guanidiniocarbonylpyrrole (GCP) unit at the lysine side chain. All peptides are composed of polar (GCP) and non-polar (cyclohexyl alanine) residues but differ in their sequence periodicity, resulting in different secondary as well as supramolecular structures. CD spectra revealed the assembly of β-sheet-, α-helical and random structures for peptides 1, 2 and 3, respectively. Consequently, this enabled the formation of distinct supramolecular assemblies such as fibres, nanorod-like or spherical aggregates. Notably, all three cationic peptides are equipped with the anion-binding GCP unit and thus possess a nucleic acid-binding centre. However, only the helical (2) and the unstructured (3) peptide were able to assemble into small virus-like DNA-polyplexes and effectively deliver DNA into cells. Notably, as both peptides (2 and 3) were also capable of siRNA-delivery, they could be utilized to downregulate expression of the caner-relevant protein Survivin.

Molecular Insight into the β-Sheet Twist and Related Morphology of Self-Assembled Peptide Amphiphile Ribbons

Self-assembly of high-aspect-ratio filaments containing β-sheets has attracted much attention due to potential use in bioengineering and biomedicine. However, precisely predicting the assembled morphologies remains a grand challenge because of insufficient understanding of the self-assembly process. We employed an atomistic model to study the self-assembly of peptide amphiphiles (PAs) containing valine-glutamic acid (VE) dimeric repeats. By changing of the sequence length, the assembly morphology changes from flat ribbon to left-handed twisted ribbon, implying a relationship between β-sheet twist and strength of interstrand hydrogen bonds. The calculations are used to quantify this relationship including both magnitude and sign of the ribbon twist angle. Interestingly, a change in chirality is observed when we introduce the RGD epitope into the C-terminal of VE repeats, suggesting arginine and glycine's role in suppressing right-handed β-sheet formation. This study provides insight into the relationship between β-sheet twist and self-assembled nanostructures including a possible design rule for PA self-assembly.

Peptide-Protein Interactions: From Drug Design to Supramolecular Biomaterials

The self-recognition and self-assembly of biomolecules are spontaneous processes that occur in Nature and allow the formation of ordered structures, at the nanoscale or even at the macroscale, under thermodynamic and kinetic equilibrium as a consequence of specific and local interactions. In particular, peptides and peptidomimetics play an elected role, as they may allow a rational approach to elucidate biological mechanisms to develop new drugs, biomaterials, catalysts, or semiconductors. The forces that rule self-recognition and self-assembly processes are weak interactions, such as hydrogen bonding, electrostatic attractions, and van der Waals forces, and they underlie the formation of the secondary structure (e.g., α-helix, β-sheet, polyproline II helix), which plays a key role in all biological processes. Here, we present recent and significant examples whereby design was successfully applied to attain the desired structural motifs toward function. These studies are important to understand the main interactions ruling the biological processes and the onset of many pathologies. The types of secondary structure adopted by peptides during self-assembly have a fundamental importance not only on the type of nano- or macro-structure formed but also on the properties of biomaterials, such as the types of interaction, encapsulation, non-covalent interaction, or covalent interaction, which are ultimately useful for applications in drug delivery.

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.

Temperature-Dependent Reversible Morphological Transformations in N-Oleoyl β-d-Galactopyranosylamine

Amphiphilic molecules self-assemble into supramolecular structures of various sizes and morphologies depending on their molecular packing and external factors. Transformations between various self-assembled morphologies are a matter of great fundamental interest. Recently, we reported the discovery of a novel class of single-chain galactopyranosylamide amphiphiles that self-assemble to form vesicles in water. Here, we describe how the vesicles composed of the amphiphile N-oleoyl β-d-galactopyranosylamine (GOA) undergo a morphological transition to fibers consisting of mainly flat sheet-like structures. Moreover, we show that this transformation is reversible in a temperature-dependent manner. We used several optical microscopy and electron microscopy techniques, circular dichroism spectroscopy, small-angle X-ray scattering, and differential scanning calorimetry, to fully investigate and characterize the morphological transformations of GOA and provide a structural basis for such phenomena. These studies provide significant molecular insight into the structural polymorphism of sugar-based amphiphiles and foresee future applications in rational design of self-assembled materials.

A review on recent advances in polymer and peptide hydrogels

In this review, we focus on the very recent developments on the use of the stimuli responsive properties of polymer hydrogels for targeted drug delivery, tissue engineering, and biosensing utilizing their different optoelectronic properties. Besides, the stimuli-responsive hydrogels, the conducting polymer hydrogels are discussed, with specific attention to the energy generation and storage behavior of the xerogel derived from the hydrogel. The electronic and ionic conducting gels have been discussed that have applications in various electronic devices, e.g., organic field effect transistors, soft robotics, ionic skins, and sensors. The properties of polymer hybrid gels containing carbon nanomaterials have been exemplified here giving attention to applications in supercapacitors, dye sensitized solar cells, photocurrent switching, etc. Recent trends in the properties and applications of some natural polymer gels to produce thermal and acoustic insulating materials, drug delivery vehicles, self-healing material, tissue engineering, etc., are discussed. Besides the polymer gels, peptide gels of different dipeptides, tripeptides, oligopeptides, polypeptides, cyclic peptides, etc., are discussed, giving attention mainly to biosensing, bioimaging, and drug delivery applications. The properties of peptide-based hybrid hydrogels with polymers, nanoparticles, nucleotides, fullerene, etc., are discussed, giving specific attention to drug delivery, cell culture, bio-sensing, and bioimaging properties. Thus, the present review delineates, in short, the preparation, properties, and applications of different polymer and peptide hydrogels prepared in the past few years.

Self-Assembled Nanostructures Regulate H2S Release from Constitutionally Isomeric Peptides

We report here on three constitutionally isomeric peptides, each of which contains two glutamic acid residues and two lysine residues functionalized with S-aroylthiooximes (SATOs), termed peptide-H2S donor conjugates (PHDCs). SATOs decompose in the presence of cysteine to generate hydrogen sulfide (H2S), a biological signaling gas with therapeutic potential. The PHDCs self-assemble in aqueous solution into different morphologies, two into nanoribbons of different dimensions and one into a rigid nanocoil. The rate of H2S release from the PHDCs depends on the morphology, with the nanocoil-forming PHDC exhibiting a complex release profile driven by morphological changes promoted by SATO decomposition. The nanocoil-forming PHDC mitigated the cardiotoxicity of doxorubicin more effectively than its nanoribbon-forming constitutional isomers as well as common H2S donors. This strategy opens up new avenues to develop H2S-releasing biomaterials and highlights the interplay between structure and function from the molecular level to the nanoscale.

Structure-Stability-Function Mechanistic Links in the Anti-Measles Virus Action of Tocopherol-Derivatized Peptide Nanoparticles

Measles remains one of the leading causes of child mortality worldwide and is re-emerging in some countries due to poor vaccine coverage, concomitant with importation of measles virus (MV) from endemic areas. The lack of specific chemotherapy contributes to negative outcomes, especially in infants or immunodeficient individuals. Fusion inhibitor peptides derived from the MV Fusion protein C-terminal Heptad Repeat (HRC) targeting MV envelope fusion glycoproteins block infection at the stage of entry into host cells, thus preventing viral multiplication. To improve efficacy of such entry inhibitors, we have modified a HRC peptide inhibitor by introducing properties of self-assembly into nanoparticles (NP) and higher affinity for both viral and cell membranes. Modification of the peptide consisted of covalent grafting with tocopherol to increase amphipathicity and lipophilicity (HRC5). One additional peptide inhibitor consisting of a peptide dimer grafted to tocopherol was also used (HRC6). Spectroscopic, imaging, and simulation techniques were used to characterize the NP and explore the molecular basis for their antiviral efficacy. HRC5 forms micellar stable NP while HRC6 aggregates into amorphous, loose, unstable NP. Interpeptide cluster bridging governs NP assembly into dynamic metastable states. The results are consistent with the conclusion that the improved efficacy of HRC6 relative to HRC5 can be attributed to NP instability, which leads to more extensive partition to target membranes and binding to viral target proteins.

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.

Self-assembly of peptide amphiphiles for drug delivery: the role of peptide primary and secondary structures

Peptide amphiphiles (PAs), functionalized with alkyl chains, are capable of self-assembling into various nanostructures. Recently, PAs have been considered as ideal drug carriers due to their good biocompatibility, specific biological functions, and hypotoxicity to normal cells and tissues. Meanwhile, the nanocarriers formed by PAs are able to achieve controlled drug release and enhanced cell uptake in response to the stimulus of the physiological environment or specific biological factors in the location of the lesion. However, the underlying detailed drug delivery mechanism, especially from the aspect of primary and secondary structures of PAs, has not been systematically summarized or discussed. Focusing on the relationship between the primary and secondary structures of PAs and stimuli-responsive drug delivery applications, this review highlights the recent advances, challenges, and opportunities of PA-based functional drug nanocarriers, and their potential pharmaceutical applications are discussed.

Self-assembly of model short triblock amphiphiles in dilute solution

In this work, a molecular theory is used to study the self-assembly of short diblock and triblock amphiphiles, with head-tail and head-linker-tail structures, respectively. The theory was used to systematically explore the effects of the molecular architecture and the affinity of the solvent for the linker and tail blocks on the relative stability of the different nanostructures formed by the amphiphiles in dilute solution, which include spherical micelles, cylindrical fibers and planar lamellas. Moreover, the theory predicts that each of these nanostructures can adopt two different types of internal organization: (i) normal nanostructures with a core composed of tail segments and a corona composed of head segments, and (ii) nanostructures with a core formed by linker segments and a corona formed by tail and head segments. The theory predicts the occurrence of a transition from micelle to fiber to lamella when increasing the length of the tail or the linker blocks, which is in qualitative agreement with the geometric packing theory and with experiments in the literature. The theory also predicts a transition from micelle to fiber to lamella as the affinity of the solvent for the tail or linker block is decreased. This result is also in qualitative agreement with experiments in the literature but cannot be explained in terms of the geometric packing theory. The molecular theory provides an explanation for this result in terms of the competition between solvophobic attractions among segments in the core and steric repulsions between segments in the corona for the different types of self-assembled nanostructures.

Coarse-grained molecular dynamics studies of the structure and stability of peptide-based drug amphiphile filaments

Peptide-based supramolecular filaments, in particular filaments self-assembled by drug amphiphiles (DAs), possess great potential in the field of drug delivery. These filaments possess one hundred percent drug loading, with a release mechanism that can be tuned based on the dissociation of the supramolecular filaments and the degradation of the DAs [Cheetham et al., J. Am. Chem. Soc., 2013, 135(8), 2907]. Recently, much attention has been drawn to the competing intermolecular interactions that drive the self-assembly of peptide-based amphiphiles into supramolecular filaments. Recently, we reported on long-time atomistic molecular dynamics simulations to characterize the structure and growth of chiral filaments by the self-assembly of a DA containing the aromatic anti-cancer drug camptothecin [Kang et al., Macromolecules, 2016, 49(3), 994]. We found that the π-π stacking of the aromatic drug governs the early stages of the self-assembly process, while also contributing towards the chirality of the self-assembled filament. Based on these all-atomistic simulations, we now build a chemically accurate coarse-grained model that can capture the structure and stability of these supramolecular filaments at long time-scales (microseconds). These coarse-grained models successfully recapitulate the growth of the molecular clusters (and their elongation trends) compared with previously reported atomistic simulations. Furthermore, the interfacial structure and the helicity of the filaments are conserved. Next, we focus on characterization of the disassembly process of a 0.675 μm DA filament at microsecond time-scales. These results provide very useful tools for the rational design of functional supramolecular filaments, in particular supramolecular filaments for drug delivery applications.

Molecular simulations of peptide amphiphiles

This review describes recent progress in the area of molecular simulations of peptide assemblies, including peptide-amphiphiles and drug-amphiphiles. The ability to predict the structure and stability of peptide self-assemblies from the molecular level up is vital to the field of nanobiotechnology. Computational methods such as molecular dynamics offer the opportunity to characterize intermolecular forces between peptide-amphiphiles that are critical to the self-assembly process. Furthermore, these computational methods provide the ability to computationally probe the structure of these supramolecular assemblies at the molecular level, which is a challenge experimentally. Herein, we briefly highlight progress in the areas of all-atomistic and coarse-grained simulation studies investigating the self-assembly process of short peptides and peptide amphiphiles. We also discuss recent all-atomistic and coarse-grained simulations of the self-assembly of a drug-amphiphile into elongated filaments. Next, we discuss how these computational methods can provide further insight into the pathway of cylindrical nanofiber formation and predict their biocompatibility by studying the interaction of these peptide-amphiphile nanostructures with model cell membranes.

All-Atom Molecular Dynamics Simulations of Peptide Amphiphile Assemblies That Spontaneously Form Twisted and Helical Ribbon Structures

Self-assembly of peptide amphiphiles (PAs) has been an active research area as the assemblies can be programmed into variously shaped nanostructures. Although cylindrical micelles are common structures, gold-binding peptide conjugates can self-assemble into chiral nanofibers with single or double helices. When gold nanoparticles bind to the helices, the resulting chiral nanoparticle assemblies have a collective plasmonic circular dichroism signal that can serve as nanoscale circular polarizers or chiroptical sensors. A better atomic-level understanding of the factors which lead to helical PA assemblies is therefore of significant importance. In this study we show that all-atom molecular dynamics simulations can describe the spontaneous structural transformation from a planar assembly of PAs to a twisted assembly or to a helical ribbon. The twist angle and the helical diameter calculated from the simulations closely match the experimental results, with the oxidation of a single Met residue in each PA leading to a change from bilayer to monolayer assemblies with significantly different ribbon properties. A secondary structure analysis shows how a combination of β-sheet formation near the hydrophobic core of the micelle and PPII structures from proline-rich C-terminus regions favors helix formation. The simulations presented here demonstrate the capability of predicting self-assembly in chiral structures, protocols that can easily be applied to the assembly of other amphiphilic molecules.

A Peptide Amphiphile Organogelator of Polar Organic Solvents

A peptide amphiphile is reported, that gelates a range of polar organic solvents including acetonitrile/water, N,N-dimethylformamide and acetone, in a process dictated by β-sheet interactions and facilitated by the presence of an alkyl chain. Similarities with previously reported peptide amphiphile hydrogelators indicate analogous underlying mechanisms of gelation and structure-property relationships, suggesting that peptide amphiphile organogel design may be predictably based on hydrogel precedents.

Multiscale simulations for understanding the evolution and mechanism of hierarchical peptide self-assembly

Multiscale molecular simulations that combine and systematically link several hierarchies can provide insights into the evolution and dynamics of hierarchical peptide self-assembly from the molecular level to the mesoscale.

Molecular packing and the handedness of the self-assemblies of C17H35CO-Ala-Phe sodium salts

Molecular packing structure dominates the handedness of the self-assemblies of a series of lipodipeptide sodium salts.

Self-assembled peptide nanostructures for functional materials

Nature is an important inspirational source for scientists, and presents complex and elegant examples of adaptive and intelligent systems created by self-assembly. Significant effort has been devoted to understanding these sophisticated systems. The self-assembly process enables us to create supramolecular nanostructures with high order and complexity, and peptide-based self-assembling building blocks can serve as suitable platforms to construct nanostructures showing diverse features and applications. In this review, peptide-based supramolecular assemblies will be discussed in terms of their synthesis, design, characterization and application. Peptide nanostructures are categorized based on their chemical and physical properties and will be examined by rationalizing the influence of peptide design on the resulting morphology and the methods employed to characterize these high order complex systems. Moreover, the application of self-assembled peptide nanomaterials as functional materials in information technologies and environmental sciences will be reviewed by providing examples from recently published high-impact studies.

Effects of Concentration and Temperature on DNA Hybridization by Two Closely Related Sequences via Large-Scale Coarse-Grained Simulations

A newly developed coarse-grained model called BioModi is utilized to elucidate the effects of temperature and concentration on DNA hybridization in self-assembly. Large-scale simulations demonstrate that complementary strands of either the tetrablock sequence or randomized sequence with equivalent number of cytosine or guanine nucleotides can form completely hybridized double helices. Even though the end states are the same for the two sequences, there exist multiple kinetic pathways that are populated with a wider range of transient aggregates of different sizes in the system of random sequences compared to that of the tetrablock sequence. The ability of these aggregates to undergo the strand displacement mechanism to form only double helices depends upon the temperature and DNA concentration. On one hand, low temperatures and high concentrations drive the formation and enhance stability of large aggregating species. On the other hand, high temperatures destabilize base-pair interactions and large aggregates. There exists an optimal range of moderate temperatures and low concentrations that allow minimization of large aggregate formation and maximization of fully hybridized dimers. Such investigation on structural dynamics of aggregating species by two closely related sequences during the self-assembly process demonstrates the importance of sequence design in avoiding the formation of metastable species. Finally, from kinetic modeling of self-assembly dynamics, the activation energy for the formation of double helices was found to be in agreement with experimental results. The framework developed in this work can be applied to the future design of DNA nanostructures in both fields of structural DNA nanotechnology and dynamic DNA nanotechnology wherein equilibrium end states and nonequilibrium dynamics are equally important requiring investigation in cooperation.