Directing the self-assembly of supra-biomolecular nanotubes using entropic forces

Development of nano-delivery systems for loaded bioactive compounds: using molecular dynamics simulations

Over the past decade, a remarkable surge in the development of functional nano-delivery systems loaded with bioactive compounds for healthcare has been witnessed. Notably, the demanding requirements of high solubility, prolonged circulation, high tissue penetration capability, and strong targeting ability of nanocarriers have posed interdisciplinary research challenges to the community. While extensive experimental studies have been conducted to understand the construction of nano-delivery systems and their metabolic behavior in vivo, less is known about these molecular mechanisms and kinetic pathways during their metabolic process in vivo, and lacking effective means for high-throughput screening. Molecular dynamics (MD) simulation techniques provide a reliable tool for investigating the design of nano-delivery carriers encapsulating these functional ingredients, elucidating the synthesis, translocation, and delivery of nanocarriers. This review introduces the basic MD principles, discusses how to apply MD simulation to design nanocarriers, evaluates the ability of nanocarriers to adhere to or cross gastrointestinal mucosa, and regulates plasma proteins in vivo. Moreover, we presented the critical role of MD simulation in developing delivery systems for precise nutrition and prospects for the future. This review aims to provide insights into the implications of MD simulation techniques for designing and optimizing nano-delivery systems in the healthcare food industry.

Size Control of On-Surface Self-Assembled Nanochains Using Soft Building Blocks

Owing to their conformational flexibility, soft molecules with side chains play a crucial role in molecular self-assembly or self-organization processes toward bottom-up building of supramolecular nanostructures. However, the influence of the rotating side chains in the confined space and subsequent surface-confined supramolecular self-assembly remains rarely explored. Herein, using the spatial confinement effect between soft building blocks, we realized size control on surface-confined supramolecular coordination self-assembly through the synergy between the repulsive steric hindrance and the attractive chemical interactions. Combining scanning tunneling microscopy with density functional theory calculations and Monte Carlo simulations, we elucidated the effective repulsive force generated by the thermal wiggling motions of the soft building blocks, allowing length tuning of the self-assembled chain structures. Through a delicate balance between the repulsive interaction induced by the spatial confinement effect and the coordinate chemical interaction, we provide a new strategy for controlling the geometry of the on-surface supramolecular nanostructures.

Investigating the Impact of Hydrophobic Polymer Segments on the Self-Assembly Behavior of Supramolecular Cyclic Peptide Systems via Asymmetric-Flow Field Flow Fractionation

The present study examines the behavior of cyclic peptide polymer conjugates that have been designed to combine their self-assembling ability via H-bonding with the properties of amphiphilic diblock copolymers. Using a combination of asymmetric flow-field flow fractionation (AF4) and small-angle neutron scattering (SANS), we have uncovered unique insight based on the population of structures established at a 24 h equilibrium profile. Our results determine that by introducing a small quantity of hydrophobicity into the conjugated polymer corona, the resulting nanotube structures exhibit low unimer dissociation which signifies enhanced stability. Furthermore, as the hydrophobicity of the polymer corona is increased, the elongation of the nanotubes is observed due to an increase in the association of unimers. This encompasses not only the H-bonding of unimers into nanotubes but also the self-assembly of single nanotubes into segmented-nanotube structures with high aspect ratios. However, this influence relies on a subtle balance between the hydrophobicity and hydrophilicity of the polymer corona. This balance is proposed to determine the solvent entropic penalty of hydrating the system, whereby the cost scales with the hydrophobic quantity. Consequently, it has been suggested that at a critical hydrophobic quantity, the solvation penalty becomes high enough such that the self-assembly of the system deviates from ordered hydrogen bonding. The association behavior is instead dominated by the hydrophobic effect which results in the undesirable formation of disordered aggregates.

Molecular Simulations of PEGylated Biomolecules, Liposomes, and Nanoparticles for Drug Delivery Applications

Since the first polyethylene glycol (PEG)ylated protein was approved by the FDA in 1990, PEGylation has been successfully applied to develop drug delivery systems through experiments, but these experimental results are not always easy to interpret at the atomic level because of the limited resolution of experimental techniques. To determine the optimal size, structure, and density of PEG for drug delivery, the structure and dynamics of PEGylated drug carriers need to be understood close to the atomic scale, as can be done using molecular dynamics simulations, assuming that these simulations can be validated by successful comparisons to experiments. Starting with the development of all-atom and coarse-grained PEG models in 1990s, PEGylated drug carriers have been widely simulated. In particular, recent advances in computer performance and simulation methodologies have allowed for molecular simulations of large complexes of PEGylated drug carriers interacting with other molecules such as anticancer drugs, plasma proteins, membranes, and receptors, which makes it possible to interpret experimental observations at a nearly atomistic resolution, as well as help in the rational design of drug delivery systems for applications in nanomedicine. Here, simulation studies on the following PEGylated drug topics will be reviewed: proteins and peptides, liposomes, and nanoparticles such as dendrimers and carbon nanotubes.

Systematic study of the structural parameters affecting the self-assembly of cyclic peptide-poly(ethylene glycol) conjugates

Self-assembling cyclic peptides (CP) consisting of amino acids with alternating d- and l-chirality form nanotubes by hydrogen bonding, hydrophobic interactions, and π-π stacking in solution. These highly dynamic materials are emerging as promising supramolecular systems for a wide range of biomedical applications. Herein, we discuss how varying the polymer conformation (linear vs. brush), as well as the number of polymer arms per peptide unimer affects the self-assembly of PEGylated cyclic peptides in different solvents, using small angle neutron scattering. Using the derived information, strong correlations were drawn between the size of the aggregates, solvent polarity, and its ability to compete for hydrogen bonding interactions between the peptide unimers. Using these data, it could be possible to engineer cyclic peptide nanotubes of a controlled length.

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.

Mechanical Reinforcement of Proteins with Polymer Conjugation

Conjugating poly(ethylene glycol) (PEG) to peptides, also known as PEGylation, is proven to increase the thermodynamical stability of peptides, and has been successfully applied to prolong the lifetime of peptide-based vaccines and therapeutic agents. While it is known that protein structure and function can be altered by mechanical stress, whether PEGylation can reinforce proteins against mechanical unfolding remains to be ascertained. Here, we illustrate that PEGylation prolongs the lifetime of α-helices subject to constant stress. PEGylation is found to increase the unfolding time through two mechanisms. We see that (1) the unfolding rate of a helical segment is decreased through prolonged plateau regimes where the peptide helical content remains constant, and (2) the proportion of refolding to unfolding is increased, primarily by shielding water molecules from replacing forcibly exposed backbone hydrogen bonds near the conjugation site. Our findings demonstrate the feasibility of improving peptide mechanical stability with polymer conjugation. This provides a basis for future studies on optimizing conjugation location and chemistry to build custom biomolecules with unforeseen mechanical functions and stability.

Understanding emergent functions in self-assembled fibrous networks

Understanding self-assembly processes of nanoscale building blocks and characterizing their properties are both imperative for designing new hierarchical, network materials for a wide range of structural, optoelectrical, and transport applications. Although the characterization and choices of these material building blocks have been well studied, our understanding of how to precisely program a specific morphology through self-assembly still must be significantly advanced. In the recent study by Xie et al (2015 Nanotechnology 26 205602), the self-assembly of end-functionalized nanofibres is investigated using a coarse-grained molecular model and offers fundamental insight into how to control the structural morphology of nanofibrous networks. Varying nanoscale networks are observed when the molecular interaction strength is changed and the findings suggest that self-assembly through the tuning of molecular interactions is a key strategy for designing nanostructured networks with specific topologies.

Hierarchical cascades of instability govern the mechanics of coiled coils: helix unfolding precedes coil unzipping

Coiled coils are a fundamental emergent motif in proteins found in structural biomaterials, consisting of α-helical secondary structures wrapped in a supercoil. A fundamental question regarding the thermal and mechanical stability of coiled coils in extreme environments is the sequence of events leading to the disassembly of individual oligomers from the universal coiled-coil motifs. To shed light on this phenomenon, here we report atomistic simulations of a trimeric coiled coil in an explicit water solvent and investigate the mechanisms underlying helix unfolding and coil unzipping in the assembly. We employ advanced sampling techniques involving steered molecular dynamics and metadynamics simulations to obtain the free-energy landscapes of single-strand unfolding and unzipping in a three-stranded assembly. Our comparative analysis of the free-energy landscapes of instability pathways shows that coil unzipping is a sequential process involving multiple intermediates. At each intermediate state, one heptad repeat of the coiled coil first unfolds and then unzips due to the loss of contacts with the hydrophobic core. This observation suggests that helix unfolding facilitates the initiation of coiled-coil disassembly, which is confirmed by our 2D metadynamics simulations showing that unzipping of one strand requires less energy in the unfolded state compared with the folded state. Our results explain recent experimental findings and lay the groundwork for studying the hierarchical molecular mechanisms that underpin the thermomechanical stability/instability of coiled coils and similar protein assemblies.

Molecular dynamics studies of PEGylated α-helical coiled coils and their self-assembled micelles

We performed coarse-grained (CG) molecular dynamics simulations of trimeric α-helical coiled coils grafted with poly(ethylene glycol) (PEG) of different sizes and conjugate positions and the self-assembled micelle of amphiphilic trimers. The CG model for the trimeric coiled coil is verified by comparing the α-helical structure and interhelical distance with those calculated from all-atom simulations. In CG simulations of PEGylated trimers, the end-to-end distances and radii of gyration of PEGs grafted to the sides of peptides become shorter than those of free PEGs in water, which agrees with experiments. This shorter size of the grafted PEGs is also confirmed by calculating the thickness of the PEG layer, which is less than the size of the mushroom. These indicate the adsorption of PEG chains onto coiled coils since hydrophobic residues in the exterior sites of coiled coils tend to be less exposed to water and thus interact with PEGs, leading to the compact conformation of adsorbed PEGs. Simulations of the self-assembly of amphiphilic trimers show that the randomly distributed trimers self-assemble to micelles. The outer radius and hydrodynamic radius of the micelle, which were calculated respectively from radial densities and diffusion coefficients, are ∼7 nm, in agreement with the experimental value of ∼7.5 nm, while the aggregation number of amphiphilic molecules per micelle is lower than the experimentally proposed value. These simulations predict the experimentally measured size of PEGs grafted to the trimeric coiled coils and their self-assembled amphiphilic micelles and suggest that the aggregation number of the micelle may be lower, which needs to be confirmed by experiments.

Thermodynamics versus Kinetics Dichotomy in the Linear Self-Assembly of Mixed Nanoblocks

We report classical and replica exchange molecular dynamics simulations that establish the mechanisms underpinning the growth kinetics of a binary mix of nanorings that form striped nanotubes via self-assembly. A step-growth coalescence model captures the growth process of the nanotubes, which suggests that high aspect ratio nanostructures can grow by obeying the universal laws of self-similar coarsening, contrary to systems that grow through nucleation and elongation. Notably, striped patterns do not depend on specific growth mechanisms, but are governed by tempering conditions that control the likelihood of depropagation and fragmentation.