Role of hydrophobicity on self-assembly by peptide amphiphiles via molecular dynamics simulations

Multiscale Simulations of Self-Assembling Peptides: Surface and Core Hydrophobicity Determine Fibril Stability and Amyloid Aggregation

Assemblies of peptides and proteins through specific intermolecular interactions set the basis for macroscopic materials found in nature. Peptides provide easily tunable hydrogen-bonding interactions, which can lead to the formation of ordered structures such as highly stable β-sheets that can form amyloid-like supramolecular peptide nanofibrils (PNFs). PNFs are of special interest, as they could be considered as mimics of various fibrillar structures found in nature. In their ability to serve as supramolecular scaffolds, they could mimic certain features of the extracellular matrix to provide stability, interact with pathogens such as virions, and transduce signals between the outside and inside of cells. Many PNFs have been reported that reveal rich bioactivities. PNFs supporting neuronal cell growth or lentiviral gene transduction have been studied systematically, and their material properties were correlated to bioactivities. However, the impact of the structure of PNFs, their dynamics, and stabilities on their unique functions is still elusive. Herein, we provide a microscopic view of the self-assembled PNFs to unravel how the amino acid sequence of self-assembling peptides affects their secondary structure and dynamic properties of the peptides within supramolecular fibrils. Based on sequence truncation, amino acid substitution, and sequence reordering, we demonstrate that peptide-peptide aggregation propensity is critical to form bioactive β-sheet-rich structures. In contrast to previous studies, a very high peptide aggregation propensity reduces bioactivity due to intermolecular misalignment and instabilities that emerge when fibrils are in close proximity to other fibrils in solution. Our multiscale simulation approach correlates changes in biological activity back to single amino acid modifications. Understanding these relationships could lead to future material discoveries where the molecular sequence predictably determines the macroscopic properties and biological activity. In addition, our studies may provide new insights into naturally occurring amyloid fibrils in neurodegenerative diseases.

Supramolecular self-assembled peptide-engineered nanofibers: A propitious proposition for cancer therapy

Cancer is a devastating disease that causes a substantial number of deaths worldwide. Current therapeutic interventions for cancer include chemotherapy, radiation therapy, or surgery. These conventional therapeutic approaches are associated with disadvantages such as multidrug resistance, destruction of healthy tissues, and tissue toxicity. Therefore, there is a paradigm shift in cancer management wherein nanomedicine-based novel therapeutic interventions are being explored to overcome the aforementioned disadvantages. Supramolecular self-assembled peptide nanofibers are emerging drug delivery vehicles that have gained much attention in cancer management owing to their biocompatibility, biodegradability, biomimetic property, stimuli-responsiveness, transformability, and inherent therapeutic property. Supramolecules form well-organized structures via non-covalent linkages, the intricate molecular arrangement helps to improve tissue permeation, pharmacokinetic profile and chemical stability of therapeutic agents while enabling targeted delivery and allowing efficient tumor imaging. In this review, we present fundamental aspects of peptide-based self-assembled nanofiber fabrication their applications in monotherapy/combinatorial chemo- and/or immuno-therapy to overcome multi-drug resistance. The role of self-assembled structures in targeted/stimuli-responsive (pH, enzyme and photo-responsive) drug delivery has been discussed along with the case studies. Further, recent advancements in peptide nanofibers in cancer diagnosis, imaging, gene therapy, and immune therapy along with regulatory obstacles towards clinical translation have been deliberated.

Lipopeptides development in cosmetics and pharmaceutical applications: A comprehensive review

Lipopeptides are surface active, natural products of bacteria, fungi and green-blue algae origin, having diverse structures and functionalities. In analogy, a number of chemical synthesis techniques generated new designer lipopeptides with desirable features and functions. Lipopetides are self-assembly guided, supramolecular compounds which have the capacity of high-density presentation of the functional epitopes at the surface of the nanostructures. This feature contributes to their successful application in several industry sectors, including food, feed, personal care, and pharmaceutics. In this comprehensive review, the novel class of ribosomally synthesized lipopeptides is introduced alongside the more commonly occuring non-ribosomal lipopeptides. We highlight key representatives of the most researched as well as recently described lipopeptide families, with emphasis on structural features, self-assembly and associated functions. The common biological, chemical and hybrid production routes of lipopeptides, including prominent analogues and derivatives are also discussed. Furthermore, genetic engineering strategies aimed at increasing lipopeptide yields, diversity and biological activity are summarized and exemplified. With respect to application, this work mainly details the potential of lipopeptides in personal care and cosmetics industry as cleansing agents, moisturizer, anti-aging/anti-wrinkling, skin whitening and preservative agents as well as the pharmaceutical industry as anitimicrobial agents, vaccines, immunotherapy, and cancer drugs. Given that this review addresses human applications, we conclude on the topic of safety of lipopeptide formulations and their sustainable production.

Recent Advancements in Enzyme‐Incorporated Nanomaterials: Synthesis, Mechanistic Formation and Applications

Over the past decade, nanotechnology has been developed and employed across various entities. Among the numerous nanostructured material types, enzyme‐incorporated nanomaterials have shown great potential in various fields, as an alternative to biologically derived as well as synthetically developed hybrid structures. The mechanism of incorporating enzyme onto a nanostructure depends on several factors including the method of immobilization, type of nanomaterial, as well as operational and environmental conditions. The prospects of enzyme‐incorporated nanomaterials have shown promising results across various applications, such as biocatalysts, biosensors, drug therapy, and wastewater treatment. This is due to their excellent ability to exhibit chemical and physical properties such as high surface‐to‐volume ratio, recovery and/or reusability rates, sensitivity, response scale, and stable catalytic activity across wide operating conditions. In this review, the evolution of enzyme‐incorporated nanomaterials along with their impact on our society due to its state‐of‐the‐art properties, and its significance across different industrial applications are discussed. In addition, the weakness and future prospects of enzyme‐incorporated nanomaterials were also discussed to guide scientists for futuristic research and development in this field.

Mapping the Morphological Landscape of Oligomeric Di-block Peptide-Polymer Amphiphiles

Peptide-polymer amphiphiles (PPAs) are tunable hybrid materials that achieve complex assembly landscapes by combining the sequence-dependent properties of peptides with the structural diversity of polymers. Despite their promise as biomimetic materials, determining how polymer and peptide properties simultaneously affect PPA self-assembly remains challenging. We herein present a systematic study of PPA structure-assembly relationships. PPAs containing oligo(ethyl acrylate) and random-coil peptides were used to determine the role of oligomer molecular weight, dispersity, peptide length, and charge density on self-assembly. We observed that PPAs predominantly formed spheres rather than anisotropic particles. Oligomer molecular weight and peptide hydrophilicity dictated morphology, while dispersity and peptide charge affected particle size. These key benchmarks will facilitate the rational design of PPAs that expand the scope of biomimetic functionality within assembled soft materials.

Recent advances in design and applications of biomimetic self-assembled peptide hydrogels for hard tissue regeneration

Abstract

The development of natural biomaterials applied for hard tissue repair and regeneration is of great importance, especially in societies with a large elderly population. Self-assembled peptide hydrogels are a new generation of biomaterials that provide excellent biocompatibility, tunable mechanical stability, injectability, trigger capability, lack of immunogenic reactions, and the ability to load cells and active pharmaceutical agents for tissue regeneration. Peptide-based hydrogels are ideal templates for the deposition of hydroxyapatite crystals, which can mimic the extracellular matrix. Thus, peptide-based hydrogels enhance hard tissue repair and regeneration compared to conventional methods. This review presents three major self-assembled peptide hydrogels with potential application for bone and dental tissue regeneration, including ionic self-complementary peptides, amphiphilic (surfactant-like) peptides, and triple-helix (collagen-like) peptides. Special attention is given to the main bioactive peptides, the role and importance of self-assembled peptide hydrogels, and a brief overview on molecular simulation of self-assembled peptide hydrogels applied for bone and dental tissue engineering and regeneration.

Graphic abstract

Pushing and Pulling: A Dual pH Trigger Controlled by Varying the Alkyl Tail Length in Heme Coordinating Peptide Amphiphiles

Some organisms in nature that undergo anaerobic respiration utilize 1D nanoscale arrays of densely packed cytochromes containing the molecule heme. The assemblies can be mimicked with 1D nanoscale fibrils composed of peptide amphiphiles designed to coordinate heme in dense arrays. To create such materials and assemblies, it is critical to understand the assembly process and what controls the various aspects of hierarchical assembly. MD simulations suggest that shorter alkyl chains on the peptide lead to more dynamic structures than the peptides with longer chains that yield kinetically trapped states. The hydration parameters manifest themselves experimentally through the observation of a dual pH trigger, which controls the peptide assembly rate, the heme binding affinity, and heme organization kinetics. Great strides in understanding the relative complexity of the self-assembly process in relation to incorporating a functional moiety like heme opens up many possibilities in developing abiotic assemblies for bioelectronic devices and assemblies.

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.

Ultrashort Peptide Self-Assembly: Front-Runners to Transport Drug and Gene Cargos

The translational therapies to promote interaction between cell and signal come with stringent eligibility criteria. The chemically defined, hierarchically organized, and simpler yet blessed with robust intermolecular association, the peptides, are privileged to make the cut-off for sensing the cell-signal for biologics delivery and tissue engineering. The signature service and insoluble network formation of the peptide self-assemblies as hydrogels have drawn a spell of research activity among the scientists all around the globe in the past decades. The therapeutic peptide market players are anticipating promising growth opportunities due to the ample technological advancements in this field. The presence of the other organic moieties, enzyme substrates and well-established protecting groups like Fmoc and Boc etc., bring the best of both worlds. Since the large sequences of peptides severely limit the purification and their isolation, this article reviews the account of last 5 years' efforts on novel approaches for formulation and development of single molecule amino acids, ultra-short peptide self-assemblies (di- and tri- peptides only) and their derivatives as drug/gene carriers and tissue-engineering systems.

ssDNA-amphiphile architecture used to control dimensions of DNA nanotubes

Controlling the dimensions of DNA nanotubes is of great interest as they can be used in different applications ranging from functional elements in nanodevices to carriers for drug delivery. ssDNA-amphiphiles composed of a ssDNA headgroup, a hydrophobic dialkyl tail and a polycarbon spacer between the tail and the headgroup, self-assemble into hollow DNA nanotubes by forming bilayer nanotapes that transition from twisted nanotapes, to helical nanotapes, to nanotubes. The presence of the DNA nanotubes is verified via cryo-TEM and SAXS. We further explore the effect of the ssDNA secondary structure and tail length on the assembly of the ssDNA-amphiphiles. We demonstrate that the presence of intermolecular G-quadruplexes in the ssDNA sequence dictates the nanotube length. The nanotube diameter is controlled by the hydrophobic tail length, and coarse-grained molecular dynamics simulations are employed to elucidate the tail design impact on assembly.

A comparison of peptide amphiphile nanofiber macromolecular assembly strategies

Supramolecular peptide nanofibers that are composed of peptide amphiphile molecules have been widely used for many purposes from biomedical applications to energy conversion. The self-assembly mechanisms of these peptide nanofibers also provide convenient models for understanding the self-assembly mechanisms of various biological supramolecular systems; however, the current theoretical models that explain these mechanisms do not sufficiently explain the experimental results. In this study, we present a new way of modeling these nanofibers that better fits with the experimental data. Molecular dynamics simulations were applied to create model fibers using two different layer models and two different tilt angles. Strikingly, the fibers which were modeled to be tilting the peptide amphiphile molecules and/or tilting the plane were found to be more stable and consistent with the experiments.

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.

Silk fibroin hydrogels for potential applications in photodynamic therapy

In this study, we prepared translucid hydrogels with different concentrations of silk fibroin, extracted from raw silk fibers, and used them as a matrix to incorporate the photosensitizer 5-(4-aminophenyl)-10,15,20-tris-(4-sulphonatophenyl) porphyrin trisodium for application in photodynamic therapy (PDT). The hydrogels obtained were characterized by rheology, spectrophotometry, and scattering techniques to elucidate the factors involved in the formation of the hydrogel, and to characterize the behavior of silk fibroin (SF) after incorporating of the porphyrin to the matrix. The rheology results demonstrated that the SF hydrogels had a shear thinning behavior. In addition, we were able to verify that the structure of the material was able to be recovered over time after shear deformation. The encapsulation of porphyrins in hydrogels leads to the formation of self-assembled peptide nanostructures that prevent porphyrin aggregation, thereby greatly increasing the generation of singlet oxygen. Also, our findings suggest that porphyrin can diffuse out of the hydrogel and permeate the outer skin layers. This evidence suggests that SF hydrogels could be used as porphyrin encapsulation and as a drug carrier for the sustained release of photosensitizers for PDT.

Hydrophobicity of surface-immobilised molecules influences architectures formed via interfacial self-assembly of nucleoside-based gelators

Surface-mediated self-assembly has potential in biomaterial development but underlying rules governing surface-gelator interactions are poorly understood. Here, we correlate surface properties with structural characterization data of nucleoside-based gels obtained by GISAXS and GIWAXS and find that hydrophobicity descriptors (log P, polar surface area, aromaticity) are key predictors for the gel structures formed.

A combination of bioactive and nonbioactive alkyl-peptides form a more stable nanofiber structure for differentiating neural stem cells: a molecular dynamics simulation survey

Self-assembling alkyl-peptides are important molecules due to their ability to construct nano-level structures such as nanofibers to be utilized as tissue engineering scaffolds. The bioactive epitope of FAQRVPP which acts as neural stem cells (NSCs) outgrowth inducing factor is used in nanofiber structures. Based on previous experimental studies the density and distribution pattern of the epitopes on the surface of the nanofibers plays an important role in the differentiation function efficiency. We decided to survey and compare the stability of two pre-constructed fiber structures in the forms of all-functionalized nanofiber (containing only bioactive alkyl-peptides) and distributed functionalized nanofiber (a combination of nonbioactive and bioactive alkyl-peptides with ratio 2:1). Our findings reveal that the all-functionalized fiber shows an unstable structure and is split into intermediate micelle-like structures to reduce compactness and steric hindrance of functional epitopes whereas the distributed functionalized fiber shows an integrated stable nanofiber with a more amount of beta sheets that are well-organized and oriented around the hydrophobic core. The hydrogen bonds and energy profiles of the structures indicate the role of hydrophobic interactions during the alkyl-chain core formation and the important role of electrostatic interactions and hydrogen bond network in the stability of the final structures. Finally, it seems that the possibility of the presence of intermediate structure is increased in the all-functionalized nanofiber environment, and it can reduce functional efficiency of the scaffolds. These findings can help to design more efficient nanofiber structures with different goals in scaffolds for tissue engineering. Abbreviations MD Molecular Dynamics NSCs Neural Stem Cells PME Particle mesh Ewald RDF Radial Distribution Function RG Radius of gyration RASA Relative Accessible Surface Area RMSD Root Mean Square Deviations SASA Solvent Accessible Surface Area. Communicated by Ramaswamy H. Sarma.

Self-assembly of peptide amphiphiles by vapor pressure osmometry and dissipative particle dynamics

Peptide amphiphiles are one of the most promising materials in the biomedical field, so much effort has been devoted to characterizing the mechanism of their self-assembly and thermosensitive gelation. In this work, vapor pressure osmometry measurements were carried out to parameterize the thermosensitivity of interactions between peptide amphiphiles in an aqueous solution. The osmometry measurement verified that the peptides became more hydrophobic as temperature increased, which was quantitatively described with the Flory-Huggins χ parameter. Thereafter, a coarse-grained molecular model was used to simulate peptide amphiphiles dissolved in an aqueous solution. The temperature sensitive coarse-grained parameter a HW, which is the repulsive force between the hydrophilic head of the peptide amphiphile and water was estimated from the aforementioned experimentally obtained χ. Furthermore, the effects of concentration and temperature on the self-assembly behavior of peptide amphiphiles were quantitatively studied by dissipative particle dynamics. The simulation results revealed that a HW plays an important role in self-assembly characteristics and in the resulting microstructure of the peptide amphiphiles, which coincides with previous experimental and computational findings. The methodology in quantitatively linking the coarse-grained parameter from experiment and theory provides a sensible foundation for bridging future simulation studies with experimental work on macromolecules.

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.

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

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

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.

Melting Behavior of Zipper-Structured Lipopeptides in Lipid Bilayer

A zipper-structured lipopeptide is expected to play a role of "intelligent valve" in the lipid bilayer. In this paper, a series of zipper-structured lipopeptides have been designed for preparing thermocontrollable hybrid liposomes. Their conformational transition as a function of temperature in lipid bilayer has been investigated for understanding the influences of molecular structure and bilayer property on biofunction. The melting temperatures T_m of the lipopeptides have been found to depend on their molecular structures. When the lipopeptides have been doped in bilayer, an increase of size of alkyl chain increases the stability of the α-helix resulting in a decrease in fluidity of lipid bilayer. However, an increase of amino groups at N-terminal is found to decrease the stability of the spatial structure. The thermocontrollability of the "valve" in lipid bilayer is confirmed by drug release experiments under different temperatures. Meanwhile, effects of bilayer properties on the thermosensitivity of lipopeptides have also been investigated. Results show the T_m of lipopeptide doped in bilayer decreases with the increase of membrane fluidity. Furthermore, the reversibility of the thermocontrolled "valve" is also proven by release drug under intermittent temperatures. It could be concluded that the molecular structure of the lipopeptide, as well as the property of bilayer, give great influence on the biofunction of the hybrid liposomes.

From Cooperative Self-Assembly to Water-Soluble Supramolecular Polymers Using Coarse-Grained Simulations

Supramolecular polymers, formed via noncovalent self-assembly of elementary monomers, are extremely interesting for their dynamic bioinspired properties. In order to understand their behavior, it is necessary to access their dynamics while maintaining high resolution in the treatment of the monomer structure and monomer-monomer interactions, which is typically a difficult task, especially in aqueous solution. Focusing on 1,3,5-benzenetricarboxamide (BTA) water-soluble supramolecular polymers, we have developed a transferable coarse-grained model that allows studying BTA supramolecular polymerization in water, while preserving remarkable consistency with the atomistic models in the description of the key interactions between the monomers (hydrophobic, H-bonding, etc.), self-assembly cooperativity, and amplification of order into the growing fibers. This permitted us to monitor the amplification of the key interactions between the monomers (including H-bonding) in the BTA fibers during the dynamic polymerization process. Our molecular dynamics simulations provide a picture of a stepwise cooperative polymerization mechanism, where initial fast hydrophobic aggregation of the BTA monomers in water is followed by the slower reorganization of these disordered aggregates into ordered directional oligomers. Supramolecular polymer growth then proceeds on a slower time scale. We challenged our models via comparison with the experimental evidence, capturing the effect of temperature variations and subtle changes in the monomer structure on the polymerization and on the properties of the fibers seen in the real systems. This work provides a multiscale spatiotemporal characterization of BTA self-assembly in water and a useful platform to study a variety of BTA-based supramolecular polymers toward structure-property relationships.

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.

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.

Self-assembly mechanisms of nanofibers from peptide amphiphiles in solution and on substrate surfaces

We report the investigation of the self-assembly mechanism of nanofibers, using a small peptide amphiphile (NapFFKYp) as a model. Combining experimental and simulation methods, we identify the self-assembly pathways in the solution and on the substrates, respectively. In the solution, peptide amphiphiles undergo the nucleation process to grow into nanofibers. The nanofibers can further twist into high-ordered nanofibers with aging. On the substrates, peptide amphiphiles form nanofibers and nanosheet structures simultaneously. This surface-induced nanosheet consists of rod-like structures, and its thickness is substrate-dependent. Most intriguingly, water can transform the nanosheet into the nanofiber. Molecular dynamic simulation suggests that hydrophobic and ion-ion interactions are dominant forces during the self-assembly process.

Extremely Stable Supramolecular Hydrogels Assembled from Nonionic Peptide Amphiphiles

Peptide hydrogels with high stability in different media are of great interest in biomedical applications. In this paper, we report an easy, fast, and scalable method for preparing a family of nonionic peptide amphiphiles (PAs) obtained by direct aminolysis of alkyl-oilgo(γ-benzyl-l-glutamate) samples, which were synthesized via the alkyl amine-initiated sequence ring-opening reaction of α-amino acid N-carboxyanhydrides. One great advantage of this method is that vast chemical diversity and large-scale yields can be achieved easily using commercially available hydramines. These PA samples can readily form a clear hydrogel without any external aid and show exceptionally enhanced gelation properties with a critical gelation concentration as low as 0.05 wt %. The hydrogels are highly stable against extreme pH values of 1 and 14 and a high salt concentration of 200 mM NaCl. These properties combined with the shear-thinning properties make these PA hydrogels ideal candidates for the new generation of injectable scaffolds.

A glycosaminoglycan mimetic peptide nanofiber gel as an osteoinductive scaffold

The self-assembling injectable bioactive peptide nanofibers have a potential therapeutic effect for acceleration of healing of bone defects.

Extracting physics of life at the molecular level: A review of single-molecule data analyses

Studying individual biomolecules at the single-molecule level has proved very insightful recently. Single-molecule experiments allow us to probe both the equilibrium and nonequilibrium properties as well as make quantitative connections with ensemble experiments and equilibrium thermodynamics. However, it is important to be careful about the analysis of single-molecule data because of the noise present and the lack of theoretical framework for processes far away from equilibrium. Biomolecular motion, whether it is free in solution, on a substrate, or under force, involves thermal fluctuations in varying degrees, which makes the motion noisy. In addition, the noise from the experimental setup makes it even more complex. The details of biologically relevant interactions, conformational dynamics, and activities are hidden in the noisy single-molecule data. As such, extracting biological insights from noisy data is still an active area of research. In this review, we will focus on analyzing both fluorescence-based and force-based single-molecule experiments and gaining biological insights at the single-molecule level. Inherently nonequilibrium nature of biological processes will be highlighted. Simulated trajectories of biomolecular diffusion will be used to compare and validate various analysis techniques.

Supramolecular chirality in self-assembled peptide amphiphile nanostructures

Induced supramolecular chirality was investigated in the self-assembled peptide amphiphile (PA) nanosystems.

Molecular dynamics simulations of self-assembled peptide amphiphile based cylindrical nanofibers

We carried out united-atom molecular dynamics simulations to understand the structural properties of peptide amphiphile (PA)-based cylindrical nanofibers and the factors that play a role in the “Self-Assembly” process on some specific nanofibers.

Self-assembly of dipeptide sodium salts derived from alanine: a molecular dynamics study

The dipeptides self-assemble into a helical structure after a 200 ns MD simulation.

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

Peptide amphiphiles are known to form a variety of distinctive self-assembled nanostructures (including cylindrical nanofibers in hydrogels) dependent upon the solvent conditions. Using a novel coarse-grained model, large-scale molecular dynamics simulations are performed on a system of 800 peptide amphiphiles (sequence, palmitoyl-Val3Ala3Glu3) to elucidate kinetic mechanisms of molecular assembly as a function of the solvent conditions. The assembly process is found to occur via a multistep process with transient intermediates that ultimately leads to the stabilized nanostructures including open networks of β-sheets, cylindrical nanofibers, and elongated micelles. Different kinetic mechanisms are compared in terms of peptide secondary structures, solvent-accessible surface area, radius of gyration, relative shape anisotropy, intra/intermolecular interactions, and aggregate size dynamics to provide insightful information for the design of functional biomaterials.