Solvent effects on kinetic mechanisms of self-assembly by peptide amphiphiles via molecular dynamics simulations

Peptide Supramolecular Self-Assembly: Regulatory Mechanism, Functional Properties, and Its Application in Foods

Peptide self-assembly, due to its diverse supramolecular nanostructures, excellent biocompatibility, and bright application prospects, has received wide interest from researchers in the fields of biomedicine and green life technology and the food industry. Driven by thermodynamics and regulated by dynamics, peptides spontaneously assemble into supramolecular structures with different functional properties. According to the functional properties derived from peptide self-assembly, applications and development directions in foods can be found and explored. Therefore, in this review, the regulatory mechanism is elucidated from the perspective of self-assembly thermodynamics and dynamics, and the functional properties and application progress of peptide self-assembly in foods are summarized, with a view to more adaptive application scenarios of peptide self-assembly in the food industry.

Anti-Glioma Activity Achieved by Dual Blood-Brain Barrier/Glioma Targeting Naive Chimeric Peptides-Based Co-Assembled Nanophototheranostics

Peptide monomers can either self-assemble with themselves enacting a solo-component assembly or they can co-assemble by interacting with other suitable partners to mediate peptide co-assembly. Peptide co-assemblies represent an innovative class of naive, multifunctional, bio-inspired supramolecular constructs that result in the production of nanostructures with widespread functional, structural, and chemical multiplicity. Herein, the co-assembly of novel chimeric peptides (conjugates of T7 (HAIYPRH)/t-Lyp-1 (CGNKRTR) peptides and aurein 1.2 (GLFDIIKKIAESF)) has been explored as a means to produce glioma theranostics exhibiting combinatorial chemo-phototherapy. Briefly, we have reported here the design and solid phase synthesis of a naive generation of twin-functional peptide drugs incorporating the blood-brain barrier (BBB) and glioma dual-targeting functionalities along with anti-glioma activity (G-Anti G and B-Anti G). Additionally, we have addressed their multicomponent co-assembly and explored their potential application as glioma drug delivery vehicles. Our naive peptide drug-based nanoparticles (NPs) successfully demonstrated a heightened glioma-specific delivery and anti-glioma activity. Multicomponent indocyanine green (ICG)-loaded peptide co-assembled NPs (PINPs: with a hydrodynamic size of 348 nm and a zeta-potential of 5 mV) showed enhanced anti-glioma responses in several cellular assays involving C6 cells. These included a mass demolition with no wound closure (i.e., a 100% cell destruction) and around 63% collaborative chemo-phototoxicity (with both a photothermal and photodynamic effect) after near infrared (NIR) 808 laser irradiation. The dual targeting ability of peptide bioconjugates towards both the BBB and glioma cells, presents new opportunities for designing tailored and better peptide-based nanostructures or nanophototheranostics for glioma.

Design of short peptides and peptide amphiphiles as collagen mimics and an investigation of their interactions with collagen using molecular dynamics simulations and docking studies

Short peptide sequences and bolaamphiphiles derived from natural proteins are gaining importance due to their ability to form unique nanoscale architectures for a variety of biological applications. In this work, we have designed six short peptides (triplet or monomeric forms) and two peptide bolaamphiphiles that either incorporate the bioactive collagen motif (Gly-X-Y) or sequences where Gly, Pro, or hydroxyproline (Hyp) are replaced by Ala or His. For the bolaamphiphiles, a malate moiety was used as the aliphatic linker for connecting His with Hyp to create collagen mimics. Stability of the assemblies was assessed through molecular dynamics simulations and results indicated that (Pro-Ala-His)₃ and (Ala-His-Hyp)₃ formed the most stable structures, while the amphiphiles and the monomers showed some disintegration over the course of the 200 ns simulation, though most regained structural integrity and formed fibrillar structures, and micelles by the end of the simulation, likely due to the formation of more thermodynamically stable conformations. Multiple replica simulations (REMD) were also conducted where the sequences were simulated at different temperatures. Our results showed excellent convergence in most cases compared to constant temperature molecular dynamics simulation. Furthermore, molecular docking and MD simulations of the sequences bound to collagen triple helix structure revealed that several of the sequences had a high binding affinity and formed stable complexes, particularly (Pro-Ala-His)₃ and (Ala-His-Hyp)₃. Thus, we have designed new hybrid-peptide-based sequences which may be developed for potential applications as biomaterials for tissue engineering or drug delivery.

Structural and photoactive properties of self-assembled peptide-based nanostructures and their optical bioapplication in food analysis

BACKGROUND

Food processing plays an important role in the modern industry because food quality and security directly affect human health, life safety, and social and economic development. Accurate, efficient, and sensitive detection technology is the basis for ensuring food quality and security. Optosensor-based technology with the advantage of fast and visual real-time detection can be used to detect pesticides, metal ions, antibiotics, and nutrients in food. As excellent optical centres, self-assembled peptide-based nanostructures possess attractive advantages, such as simple preparation methods, controllable morphology, tunable functionality, and inherent biocompatibility.

AIM OF REVIEW

Self-assembled peptide nanostructures with good fabrication yield, stability, dispersity in a complex sample matrix, biocompatibility, and environmental friendliness are ideal development goals in the future. Owing to its flexible and unique optical properties, some short peptide self-assemblies can possibly be used to achieve the purpose of rapid and sensitive detection of composition in food, agriculture, and the environment, expanding the understanding and application of peptide-based optics in analytical chemistry.

KEY SCIENTIFIC CONCEPT OF REVIEW

The self-assembly process of peptides is driven by noncovalent interactions, including hydrogen bonding, electrostatic interactions, hydrophobic interactions, and π-π stacking, which are the key factors for obtaining stable self-assembled peptide nanostructures with peptides serving as assembly units. Controllable morphology of self-assembled peptide nanostructures can be achieved through adjustment in the type, concentration, and pH of organic solvents and peptides. The highly ordered nanostructures formed by the self-assembly of peptides have been proven to be novel biological structures and can be used for the construction of optosensing platforms in biological or other systems. Optosensing platforms make use of signal changes, including optical signals and electrical signals caused by specific reactions between analytes and active substances, to determine the content or concentration of an analyte.

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.

Additives-directed lyotropic liquid crystals architecture: Simulations and experiments

In this study, alkanes and sucrose esters are employed to investigate the influence of additives on lyotropic liquid crystal architecture. After molecular dynamic simulations and experiment characterization, we showed how the additives control the structure of LLCs. By controlling the polarity of additives, the phase behavior of LLCs can be engineered to form the required structure. Dissipative particle dynamics (DPD) is introduced for simulating the self-assembly of phytantriol (PT), providing intuitionistic images and structure information, which shows that additives with low-polarity complicate the internal structure of liquid crystal systems. Then the ternary phase diagrams of additives, PT, and water are constructed to systematically study the effects of additives on the phase behavior of LLCs. Consistent with DPD simulation results, there is a certain regularity in the effects of additives on the structure of liquid crystals. The difference in the structure of LLCs is due to the variability in the critical packing parameter (CPP) obtained by changing the polarity of additives. Our findings demonstrate that additives polarity is a key factor in LLCs structure, and may pave a promising avenue for novel LLCs development and translation, determining the self-assembly process and the resulting phase of LLCs.

Solvent effects on host-guest residence time and kinetics: further insights from metadynamics simulation of Toussaintine-A unbiding from chitosan nanoparticle

Solvents play an important role in host-guest intermolecular interactions. The kinetics and residence time of Toussaintine-A (TouA) unbinding from chitosan was investigated by means of well-tempered metadynamics and thermodynamic integration using two solvents, polar aprotic (DMSO), and polar protic (water). The kinetic rates were found to be strongly dependent on the solvent polarity; hence, the unbinding rate proceeded much faster in DMSO compared to water. DMSO tends to participate less in a chemical reaction by weakening the intermolecular interaction between chitosan and TouA due to lack of acidic hydrogen resulting in a reduction of the transition state. On the other hand, water, which ought to donate hydrogen atoms, sustains a strong interaction and hence large barrier heights. Consequently, this reduces the unbinding rate and increases the residence time. Binding free energy from thermodynamic integration suggests a thermodynamic stable chitosan-TouA complex in water than in DMSO. Graphical abstract.

Control of peptide hydrogel formation and stability via heating treatment

Heating treatment is widely used in the preparation of metallic materials with controlled phase behavior and mechanical properties. However, for the soft materials assembled by short peptides, especially simple dipeptides, the detailed influences of heating treatment on the structures and functions of the materials remain largely unexplored. Here we showed that by thermal annealing or quenching of aromatic peptide solutions under kinetic control, we are able to control the self-assembly of peptide into materials with distinct phase behavior and macroscopic properties. The thermal annealing of the heated peptide solutions will lead to the formation of large nanobelts or bundles in solution, and no gels will be formed. However, by quenching the heated peptide solution, a self-supporting hydrogel will be formed quickly. Structure analysis revealed that the peptides preferred to self-assembled into much thinner and flexible nanohelices during quenching treatment. Moreover, the stability of the gels further increased with the repeated heating and quenching cycling of the peptide solutions. The results demonstrated that the heat treatment can be used to control the structure and function of self-assembled materials in a way similar to that of the conventional metallic or alloy materials.

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.

Fibrillar Network Dynamics during Oscillatory Rheology of Supramolecular Gels

Supramolecular gels are three-dimensional network structures formed by the hierarchical self-assembly of small molecules through weak noncovalent interactions. On the basis of the various interactions contributed by specific functional groups/moieties, gels with different architectures can be constructed that are smart to the external stimuli such as pH, type of solvent, stress, temperature, etc. In the present work, we explore the oscillatory shear response of supramolecular self-assembled systems formed by the low-molecular-weight (LMW) gelator based on difunctionalized amino acid, florenylmethoxycarbonyl (Fmoc)-lysine(Fmoc), Fm-K(Fm) in aqueous buffer solution, at two different pH (6 and 7.4). Small amplitude oscillatory shear (SAOS) reported weak frequency dependence of moduli indicating a gel-like network structure. Large amplitude oscillatory shear (LAOS) indicated flow regimes dictated by yielding and subsequent network dynamics analogous to cagelike soft glassy events reported for colloidal systems. The three interval thixotropy test (3iTT) indicated recovery of moduli due to regelation contributed by the reversible interactions. A generalized network model framework is utilized to investigate the transient network characteristics of the Fm-K(Fm) gels. The "network creation" and "network loss" rates were chosen as exponential functions of scaled shear stress (= |τ12(t)G|) to effectively describe the complex response. On the basis of the insights, possible mechanisms to explain the differences/similarities in the response at different pH are speculated. It is further illustrated that the modeling strategy can be extended to supramolecular gels of different classes because of the commonality/universality of their response features under oscillatory shear.

Probing mechanical properties and failure mechanisms of fibrils of self-assembling peptides

Self-assembling peptides (SAPs) are a promising class of biomaterials amenable to easy molecular design and functionalization. Despite their increasing usage in regenerative medicine, a detailed analysis of their biomechanics at the nanoscale level is still missing. In this work, we propose and validate, in all-atom dynamics, a coarse-grained model to elucidate strain distribution, failure mechanisms and biomechanical effects of functionalization of two SAPs when subjected to both axial stretching and bending forces. We highlight different failure mechanisms for fibril seeds and fibrils, as well as the negligible contribution of the chosen functional motif to the overall system rupture. This approach could lay the basis for the development of "more" coarse-grained models in the long pathway connecting SAP sequences and hydrogel mechanical properties.

Injectable peptide hydrogel as intraperitoneal triptolide depot for the treatment of orthotopic hepatocellular carcinoma

Chemotherapy is among the limited choices approved for the treatment of hepatocellular carcinoma (HCC) at intermediate and advanced stages. Preferential and prolonged drug exposure in diseased sites is required to maximize the therapeutic index of the drug. Here, we report an injectable supramolecular peptide hydrogel as an intraperitoneal depot for localized and sustained release of triptolide for the treatment of orthotopic HCC. We chose peptide amphiphile C₁₆-GNNQQNYKD-OH-based nanofibers as gelators and carriers for triptolide. Sustained triptolide release from the hydrogel was achieved over 14 days in vitro, with higher accumulation in and cytotoxicity against human HCC Bel-7402 in comparison with L-02 fetal hepatocytes. After intraperitoneal injection, the hydrogel showed prolonged retention over 13 days and preferential accumulation in the liver, realizing HCC growth inhibition by 99.7 ± 0.1% and animal median survival extension from 19 to 43 days, without causing noticeable pathological changes in the major organs. These results demonstrate that injectable peptide hydrogel can be a potential carrier for localized chemotherapy of HCC.

From Microscale to Macroscale: Nine Orders of Magnitude for a Comprehensive Modeling of Hydrogels for Controlled Drug Delivery

Because of their inherent biocompatibility and tailorable network design, hydrogels meet an increasing interest as biomaterials for the fabrication of controlled drug delivery devices. In this regard, mathematical modeling can highlight release mechanisms and governing phenomena, thus gaining a key role as complementary tool for experimental activity. Starting from the seminal contribution given by Flory-Rehner equation back in 1943 for the determination of matrix structural properties, over more than 70 years, hydrogel modeling has not only taken advantage of new theories and the increasing computational power, but also of the methods offered by computational chemistry, which provide details at the fundamental molecular level. Simulation techniques such as molecular dynamics act as a "computational microscope" and allow for obtaining a new and deeper understanding of the specific interactions between the solute and the polymer, opening new exciting possibilities for an in silico network design at the molecular scale. Moreover, system modeling constitutes an essential step within the "safety by design" paradigm that is becoming one of the new regulatory standard requirements also in the field-controlled release devices. This review aims at providing a summary of the most frequently used modeling approaches (molecular dynamics, coarse-grained models, Brownian dynamics, dissipative particle dynamics, Monte Carlo simulations, and mass conservation equations), which are here classified according to the characteristic length scale. The outcomes and the opportunities of each approach are compared and discussed with selected examples from literature.

Controlling the Self-Assembly of Biomolecules into Functional Nanomaterials through Internal Interactions and External Stimulations: A Review

Biomolecular self-assembly provides a facile way to synthesize functional nanomaterials. Due to the unique structure and functions of biomolecules, the created biological nanomaterials via biomolecular self-assembly have a wide range of applications, from materials science to biomedical engineering, tissue engineering, nanotechnology, and analytical science. In this review, we present recent advances in the synthesis of biological nanomaterials by controlling the biomolecular self-assembly from adjusting internal interactions and external stimulations. The self-assembly mechanisms of biomolecules (DNA, protein, peptide, virus, enzyme, metabolites, lipid, cholesterol, and others) related to various internal interactions, including hydrogen bonds, electrostatic interactions, hydrophobic interactions, π⁻π stacking, DNA base pairing, and ligand⁻receptor binding, are discussed by analyzing some recent studies. In addition, some strategies for promoting biomolecular self-assembly via external stimulations, such as adjusting the solution conditions (pH, temperature, ionic strength), adding organics, nanoparticles, or enzymes, and applying external light stimulation to the self-assembly systems, are demonstrated. We hope that this overview will be helpful for readers to understand the self-assembly mechanisms and strategies of biomolecules and to design and develop new biological nanostructures or nanomaterials for desired applications.

The design and biomedical applications of self-assembled two-dimensional organic biomaterials

Self-assembling 2D organic biomaterials exhibit versatile abilities for structural and functional tailoring, as well as high potential for biomedical applications.

Consequences of a cosolvent on the structure and molecular dynamics of supramolecular polymers in water

Polar cosolvents are commonly used to guide the self-assembly of amphiphiles in water. Here we investigate the influence of the cosolvent acetonitrile (ACN) on the structure and dynamics of a supramolecular polymer in water, which is based on the well-known benzene-1,3,5-tricarboxamide motif. Hydrogen/deuterium exchange mass spectroscopy measurements show that a gradual increase in the amount of ACN results in a gradual increase in the exchange dynamics of the monomers. In contrast, the morphology of the supramolecular polymers remains unchanged up to 15% of ACN, but then an abrupt change occurs and spherical aggregates are formed. Remarkably, this abrupt change coincides with the formation of micro-heterogeneity in the water-ACN mixtures. The results illustrate that in order to completely characterize supramolecular polymers it is important to add time-resolved measurements that probe their dynamic behavior, to the conventional techniques that are used to assess the morphology of the polymers. Subsequently we have used time-resolved measurements to investigate the influence of the concentration of ACN on the polymerization and depolymerization rates of the supramolecular polymers. Polymerization occurs within minutes when molecularly dissolved monomers are injected from ACN into water and is independent of the fraction of ACN up to 15%. In the depolymerization experiments-initiated by mixing equilibrated supramolecular polymers with dissolved monomers-the equilibration of the system takes multiple hours and does depend on the fraction of ACN. Interestingly, the longest equilibration time of the polymers is observed at a critical solvent composition of around 15% ACN. The differences in the timescales detected in the polymerization and depolymerization experiments are likely correlated to the non-covalent interactions involved, namely the hydrophobic effect and hydrogen-bonding interactions. We attribute the observed fast kinetics in the polymerization reactions to the hydrophobic effect, whereas the formation of intermolecular hydrogen bonds is the retarding factor in the equilibration of the polymers in the depolymerization experiments. Molecular dynamics simulations show that the latter is a likely explanation because ACN interferes with the hydrogen bonds and loosens the internal structure of the polymers. Our results highlight the importance of the solution conditions during the non-covalent synthesis of supramolecular polymers, as well as after equilibration of the polymers.

Dimensional control of supramolecular assemblies of diacetylene-derived peptide gemini amphiphile: from spherical micelles to foamlike networks

Peptide amphiphiles capable of assembling into multidimensional nanostructures have attracted much attention over the past decade due to their potential applications in materials science. Herein, a novel diacetylene-derived peptide gemini amphiphile with a fluorenylmethyloxycarbonyl (Fmoc) group at the N-terminus is reported to hierarchically assemble into spherical micelles, one-dimensional nanorods, two-dimensional foamlike networks and lamellae. Solvent polarity shows a remarkable effect on the self-assembled structures by changing the balance of four weak noncovalent interactions (hydrogen-bonding, π-π stacking, hydrophobic interaction, and electrostatic repulsion). We also show the time-evolution not only from spherical micelles to helical nanofibers in aqueous solution, but also from branched wormlike micelles to foamlike networks in methanol solution. In this work, the presence of the Fmoc group plays a key role in the self-assembly process. This work provides an efficient strategy for precise morphological control, aiding the future development in materials science.

Guiding principles for peptide nanotechnology through directed discovery

Life's diverse molecular functions are largely based on only a small number of highly conserved building blocks - the twenty canonical amino acids. These building blocks are chemically simple, but when they are organized in three-dimensional structures of tremendous complexity, new properties emerge. This review explores recent efforts in the directed discovery of functional nanoscale systems and materials based on these same amino acids, but that are not guided by copying or editing biological systems. The review summarises insights obtained using three complementary approaches of searching the sequence space to explore sequence-structure relationships for assembly, reactivity and complexation, namely: (i) strategic editing of short peptide sequences; (ii) computational approaches to predicting and comparing assembly behaviours; (iii) dynamic peptide libraries that explore the free energy landscape. These approaches give rise to guiding principles on controlling order/disorder, complexation and reactivity by peptide sequence design.

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.

Hierarchical Self-Assembly of Histidine-Functionalized Peptide Amphiphiles into Supramolecular Chiral Nanostructures

Controlling the hierarchical organization of self-assembling peptide amphiphiles into supramolecular nanostructures opens up the possibility of developing biocompatible functional supramolecular materials for various applications. In this study, we show that the hierarchical self-assembly of histidine- (His-) functionalized PAs containing d- or l-amino acids can be controlled by both solution pH and molecular chirality of the building blocks. An increase in solution pH resulted in the structural transition of the His-functionalized chiral PA assemblies from nanosheets to completely closed nanotubes through an enhanced hydrogen-bonding capacity and π-π stacking of imidazole ring. The effects of the stereochemistry and amino acid sequence of the PA backbone on the supramolecular organization were also analyzed by CD, TEM, SAXS, and molecular dynamics simulations. In addition, an investigation of chiral mixtures revealed the differences between the hydrogen-bonding capacities and noncovalent interactions of PAs with d- and l-amino acids.

Kinetics-Controlled Amphiphile Self-Assembly Processes

Amphiphile self-assembly is an essential bottom-up approach of fabricating advanced functional materials. Self-assembled materials with desired structures are often obtained through thermodynamic control. Here, we demonstrate that the selection of kinetic pathways can lead to drastically different self-assembled structures, underlining the significance of kinetic control in self-assembly. By constructing kinetic network models from large-scale molecular dynamics simulations, we show that two largely similar amphiphiles, 1-[11-oxo-11-(pyren-1-ylmethoxy)-undecyl]pyridinium bromide (PYR) and 1-(11-((5a1,8a-dihydropyren-1-yl)methylamino)-11-oxoundecyl)pyridinium bromide (PYN), prefer distinct kinetic assembly pathways. While PYR prefers an incremental growth mechanism and forms a nanotube, PYN favors a hopping growth pathway leading to a vesicle. Such preference was found to originate from the subtle difference in the distributions of hydrophobic and hydrophilic groups in their chemical structures, which leads to different rates of the adhesion process among the aggregating micelles. Our results are in good agreement with experimental results, and accentuate the role of kinetics in the rational design of amphiphile self-assembly.

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.

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.

Peptide self-assembly: thermodynamics and kinetics

Self-assembling systems play a significant role in physiological functions and have therefore attracted tremendous attention due to their great potential for applications in energy, biomedicine and nanotechnology. Peptides, consisting of amino acids, are among the most popular building blocks and programmable molecular motifs. Nanostructures and materials assembled using peptides exhibit important potential for green-life new technology and biomedical applications mostly because of their bio-friendliness and reversibility. The formation of these ordered nanostructures pertains to the synergistic effect of various intermolecular non-covalent interactions, including hydrogen-bonding, π-π stacking, electrostatic, hydrophobic, and van der Waals interactions. Therefore, the self-assembly process is mainly driven by thermodynamics; however, kinetics is also a critical factor in structural modulation and function integration. In this review, we focus on the influence of thermodynamic and kinetic factors on structural assembly and regulation based on different types of peptide building blocks, including aromatic dipeptides, amphiphilic peptides, polypeptides, and amyloid-relevant peptides.

Computational and experimental approaches for investigating nanoparticle-based drug delivery systems

Most therapeutic agents suffer from poor solubility, rapid clearance from the blood stream, a lack of targeting, and often poor translocation ability across cell membranes. Drug/gene delivery systems (DDSs) are capable of overcoming some of these barriers to enhance delivery of drugs to their right place of action, e.g. inside cancer cells. In this review, we focus on nanoparticles as DDSs. Complementary experimental and computational studies have enhanced our understanding of the mechanism of action of nanocarriers and their underlying interactions with drugs, biomembranes and other biological molecules. We review key biophysical aspects of DDSs and discuss how computer modeling can assist in rational design of DDSs with improved and optimized properties. We summarize commonly used experimental techniques for the study of DDSs. Then we review computational studies for several major categories of nanocarriers, including dendrimers and dendrons, polymer-, peptide-, nucleic acid-, lipid-, and carbon-based DDSs, and gold nanoparticles. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.

Trace Solvent as a Predominant Factor To Tune Dipeptide Self-Assembly

Solvent molecules such as water are of key importance for tuning self-assembly in biological systems. However, it remains a great challenge to detect the role of different types of noncovalent interactions between trace solvents and biomolecules such as peptides. In this work, we discover a dominant role of trace amounts of solvents for mediation of dipeptide self-assembly, in which solvent-bridged hydrogen bonding is demonstrated as a crucial force in directing fiber formation. Hydrogen-bond-forming solvents (including ethanol, N,N-dimethylformamide, and acetone) can affect the hydrogen bonding of C═O and N-H in diphenylalanine (FF) molecules with themselves, but this does not induce π-π stacking between FF molecules. The directional hydrogen bonding promotes a long-range-ordered arrangement of FF molecules, preferentially along one dimension to form nanofibers or nanobelts. Furthermore, we demonstrate that water with strong hydrogen-bond-forming capability can notably speed up structure formation with long-range order, revealing the importance of water as a trace solvent for regulation of persistent and robust fiber formation.

π-π Stacking Mediated Chirality in Functional Supramolecular Filaments

While a great diversity of peptide-based supra-molecular filaments have been reported, the impact of an auxiliary segment on the chiral assembly of peptides remains poorly understood. Herein we report on the formation of chiral filaments by the self-assembly of a peptide-drug conjugate containing an aromatic drug camptothecin (CPT) in a computational study. We find that the chirality of the filament is mediated by the π‒π stacking between CPTs, not only by the well-expected intermolecular hydrogen bonding between peptide segments. Our simulations show that π‒π stacking of CPTs governs the early stages of the self-assembly process, while a hydrogen bonding network starts at a relatively later stage to contribute to the eventual morphology of the filament. Our results also show the possible presence of water within the core of the CPT filament. These results provide very useful guiding principles for the rational design of supramolecular assemblies of peptide conjugates with aromatic segments.

Supramolecular Hydrogelators and Hydrogels: From Soft Matter to Molecular Biomaterials

In this review we intend to provide a relatively comprehensive summary of the work of supramolecular hydrogelators after 2004 and to put emphasis particularly on the applications of supramolecular hydrogels/hydrogelators as molecular biomaterials. After a brief introduction of methods for generating supramolecular hydrogels, we discuss supramolecular hydrogelators on the basis of their categories, such as small organic molecules, coordination complexes, peptides, nucleobases, and saccharides. Following molecular design, we focus on various potential applications of supramolecular hydrogels as molecular biomaterials, classified by their applications in cell cultures, tissue engineering, cell behavior, imaging, and unique applications of hydrogelators. Particularly, we discuss the applications of supramolecular hydrogelators after they form supramolecular assemblies but prior to reaching the critical gelation concentration because this subject is less explored but may hold equally great promise for helping address fundamental questions about the mechanisms or the consequences of the self-assembly of molecules, including low molecular weight ones. Finally, we provide a perspective on supramolecular hydrogelators. We hope that this review will serve as an updated introduction and reference for researchers who are interested in exploring supramolecular hydrogelators as molecular biomaterials for addressing the societal needs at various frontiers.