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Self-assembly features prominently in fields ranging from materials science to biophysical chemistry. Assembly pathways, often passing through transient intermediates, can control the outcome of assembly processes. Yet, the mechanisms of self-assembly remain largely obscure due to a lack of experimental tools for probing these pathways at the molecular level. Here, the self-assembly of self-replicators into fibers is visualized in real-time by high-speed atomic force microscopy (HS-AFM). Fiber growth requires the conversion of precursor molecules into six-membered macrocycles, which constitute the fibers. HS-AFM experiments, supported by molecular dynamics simulations, revealed that aggregates of precursor molecules accumulate at the sides of the fibers, which then diffuse to the fiber ends where growth takes place. This mechanism of precursor reservoir formation, followed by one-dimensional diffusion, which guides the precursor molecules to the sites of growth, reduces the entropic penalty associated with colocalizing precursors and growth sites and constitutes a new mechanism for supramolecular polymerization.

The possibility of using differential pre-heating prior to supramolecular gelation to control the balance between hydrogen-bonding and aromatic stacking interactions in supramolecular gels and obtain consequent systematic regulation of structure and properties is demonstrated. Using a model aromatic peptide amphiphile, Fmoc-tyrosyl-leucine (Fmoc-YL) and a combination of fluorescence, infrared, circular dichroism and NMR spectroscopy, it is shown that the balance of these interactions can be adjusted by temporary exposure to elevated temperatures in the range 313-365 K, followed by supramolecular locking in the gel state by cooling to room temperature. Distinct regimes can be identified regarding the balance between H-bonding and aromatic stacking interactions, with a transition point at 333 K. Consequently, gels can be obtained with customizable properties, including supramolecular chirality and gel stiffness. The differential supramolecular structures also result in changes in proteolytic stability, highlighting the possibility of obtaining a range of supramolecular architectures from a single molecular structure by simply controlling the pre-assembly temperature.

The self-assembly of bio-inspired supramolecular polymers can be unravelled using molecular dynamics simulations combined with 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.

Self-replication at the molecular level is often seen as essential to the early origins of life. Recently a mechanism of self-replication has been discovered in which replicator self-assembly drives the process. We have studied one of the examples of such self-assembling self-replicating molecules to a high level of structural detail using a combination of computational and spectroscopic techniques. Molecular Dynamics simulations of self-assembled stacks of peptide-derived replicators provide insights into the structural characteristics of the system and serve as the basis for semiempirical calculations of the UV-vis, circular dichroism (CD) and infrared (IR) absorption spectra that reflect the chiral organization and peptide secondary structure of the stacks. Two proposed structural models are tested by comparing calculated spectra to experimental data from electron microscopy, CD and IR spectroscopy, resulting in a better insight into the specific supramolecular interactions that lead to self-replication. Specifically, we find a cooperative self-assembly process in which β-sheet formation leads to well-organized structures, while also the aromatic core of the macrocycles plays an important role in the stability of the resulting fibers.

Designing molecular disorder Melanins are a group of natural pigments that are the primary factor affecting skin color. Lampel et al. examined a family of melanin-inspired materials based on tripeptides containing tyrosine as precursors for polymeric pigments. They found that the supramolecular organization of the tripeptide assembly is the most important factor for the enzymatic oxidation, with the position of the tyrosine residue playing a dominant role. Thus, simply juggling the order of the peptides allowed tuning of the optical and electrical properties of the resulting polymers. Science , this issue p. 1064

Stem cells are known to differentiate in response to the chemical and mechanical properties of the substrates on which they are cultured. Thus, supramolecular biomaterials with tunable properties are well suited for the study of stem cell differentiation. In this report, we exploited this phenomenon by combining stem cell differentiation in hydrogels with variable stiffness and metabolomics analysis to identify specific bioactive lipids that are uniquely used up during differentiation. To achieve this, we cultured perivascular stem cells on supramolecular peptide gels of different stiffness, and metabolite depletion followed. On soft (1 kPa), stiff (13 kPa), and rigid (32 kPa) gels, we observed neuronal, chondrogenic, and osteogenic differentiation, respectively, showing that these stem cells undergo stiffness-directed fate selection. By analyzing concentration variances of >600 metabolites during differentiation on the stiff and rigid gels (and focusing on chondrogenesis and osteogenesis as regenerative targets, respectively), we identified that specific lipids (lysophosphatidic acid and cholesterol sulfate, respectively), were significantly depleted. We propose that these metabolites are therefore involved in the differentiation process. In order to unequivocally demonstrate that the lipid metabolites that we identified play key roles in driving differentiation, we subsequently demonstrated that these individual lipids can, when fed to standard stem cell cultures, induce differentiation toward chondrocyte and osteoblast phenotypes. Our concept exploits the design of supramolecular biomaterials as a strategy for discovering cell-directing bioactive metabolites of therapeutic relevance.

For the development of applications and novel uses for peptide nanostructures, robust routes for their surface functionalization, that ideally do not interfere with their self-assembly properties, are required. Many existing methods rely on covalent functionalization, where building blocks are appended with functional groups, either pre- or post-assembly. A facile supramolecular approach is demonstrated for the formation of functionalized nanofibers by combining the advantages of biocatalytic self-assembly and surfactant/gelator co-assembly. This is achieved by enzymatically triggered reconfiguration of free flowing micellar aggregates of pre-gelators and functional surfactants to form nanofibers that incorporate and display the surfactants' functionality at the surface. Furthermore, by varying enzyme concentration, the gel stiffness and supramolecular organization of building blocks can be varied.

Self-assembled supramolecular structures of peptide derivatives often reflect a kinetically trapped state rather than the thermodynamically most favoured structure, which presents a challenge when trying to elucidate the molecular design rules for these systems. In this article we use thermodynamically controlled self-assembly, driven by enzymatic condensation of amino acid derivatives, to elucidate chemical composition/nanostructure relationships for four closely related Fmoc-dipeptide-methyl esters which form hydrogels; SF, SL, TF and TL. We demonstrate that each of the four systems self-assemble to form extended arrays of β-sheets which interlock via π-stacking of Fmoc-moieties, yet with subtle differences in molecular organisation as supported by rheology, fluorescence emission spectroscopy, infrared spectroscopy, X-ray diffraction analysis and molecular mechanics minimisation.

Aromatic peptide amphiphile hydrogelators commonly utilise the fluorenyl-9-methoxycarbonyl moiety as an N-terminal capping group. Material properties and spectroscopic techniques show the influence of alternative linkers between the fluorenyl moiety and the peptide. This study establishes whether methoxycarbonyl is an optimal or mainly convenient linker, for this class of self-assembling systems.

Peptide based 2D nanostructures of micronscale size in both X and Y dimensions are extremely rare because amino acid chirality favours helical structures, and nucleation-growth mechanisms usually favour uni-directional growth. We demonstrate the production of extended two-dimensional (2D) peptide nanostructuresvia the thermolysin catalysed condensation of Fmoc protected hydrophilic amino acid (serine, Fmoc-S) and a hydrophobic amino acid ester (phenylalanine, F-OMe). We propose that lateral self-assembly is enabled by the reversible nature of the system, favouring the thermodynamic product (extended sheets) over kinetically favoured 1 dimensional structures. Fmoc-SF-OMe forms extended arrays of β-sheet structures interlock via π-stacking between Fmoc groups. We propose that, due to its alternating hydrophilic/hydrophobic amino acid sequence, amphiphilic sheets presenting either phenyl or hydroxyl functionality are formed that assemble pair-wise, thereby shielding hydrophobic groups from the aqueous environment. Formation of these structures was supported by fluorescence emission spectroscopy, FTIR and XRD analysis and molecular mechanics minimization. At enhanced enzyme concentrations, hierarchical self-assembly was observed giving rise to spherulitic structures, with the number of spherulites dictated by enzyme concentration.