Sequence adaptive peptide-polysaccharide nanostructures by biocatalytic self-assembly

Coassembly of peptides and polysaccharides can give rise to the formation of nanostructures with tunable morphologies. We show that in situ enzymatic exchange of a dipeptide sequence in aromatic peptide amphiphiles/polysaccharide coassemblies enables dynamic formation and degradation of different nanostructures depending on the nature of the polysaccharide present. This is achieved in a one-pot system composed of Fmoc-cysteic acid (CA) and Fmoc-lysine (K) plus phenylalanine amide (F) in the presence of thermolysin that, through dynamic hydrolysis and amide formation, gives rise to a dynamic peptide library composed of the corresponding Fmoc-dipeptides (CAF and KF). When the cationic polysaccharide chitosan is added to this mixture, selective amplification of the CAF peptide is observed giving rise to formation of nanosheets through coassembly. By contrast, upon addition of anionic heparin, KF is formed that gives rise to a nanotube morphology. The dynamic adaptive potential was demonstrated by sequential morphology changes depending on the sequence of polysaccharide addition. This first demonstration of the ability to access different peptide sequences and nanostructures, depending on the presence of biopolymers, may pave the way to biomaterials that can adapt their structure and function and may be of relevance in the design of materials able to undergo dynamic morphogenesis

Emergence of function and selection from recursively programmed polymerisation reactions in mineral environments

Living systems are characterised by an ability to sustain chemical reaction networks far‐from‐equilibrium. It is likely that life first arose through a process of continual disruption of equilibrium states in recursive reaction networks, driven by periodic environmental changes allowing the emergence of a memory. Herein, we report the emergence of proto‐enzymatic function from recursive polymerisation reactions using amino acids and glycolic acid over four wet‐dry cycles. Reactions are kept out of equilibrium by diluting products 9:1 in fresh starting solution at the end of each recursive cycle, and the development of complex high molecular weight species is explored using a new metric, the Mass Index, which allows the complexity of the system to be explored as a function of cycle. This process is carried out on a range of different mineral environments. We explore the hypothesis that disrupting equilibrium via recursive cycling imposes a selection pressure and subsequent boundary conditions on products, which may otherwise be prone to uncontrolled combinatorial explosion. After just four reaction cycles, product mixtures from recursive reactions exhibit greater catalytic activity and truncation of product space towards higher molecular weight species compared to non‐recursive controls

Minimalistic supramolecular proteoglycan mimics by co-assembly of aromatic peptide and carbohydrate amphiphiles

We report the co-assembly of aromatic carbohydrate and dipeptide amphiphiles under physiological conditions as a strategy to generate minimalistic proteoglycan mimics. The resulting nanofibers present a structural, fluorenylmethoxycarbonyl-diphenylalanine (Fmoc-FF) core and a functional carbohydrate (Fmoc-glucosamine-6-sulfate or -phosphate) shell. The size, degree of bundling and mechanical properties of the assembled structures depend on the chemical nature of the carbohydrate amphiphile used. In cell culture medium, these nanofibers can further organize into supramolecular hydrogels. We demonstrate that, similar to proteoglycans, the assembled gels prolong the stability of growth factors and preserve the viability of cultured cells. Our results demonstrate that this approach can be applied to the design of extracellular matrix (ECM) substitutes for future regenerative therapies.We acknowledge the EU's H2020 and FP7 framework programmes (Forecast 668983; CHEM2NATURE 692333; THE DISCOVERIES CTR 739572; ERC AdG ComplexiTE 321266) and the Portuguese FCT (IF/00032/2013; BD/113794/2015; BPD/85790/2012; M-ERA-NET2/0001/2016 – INCIPIT; ENMed/001/2015 – CytoNanoHeal). We thank P. Frederix for his help in the FTIR measurements and M. Mullin for her help in the TEM imaging.info:eu-repo/semantics/publishedVersio

Integrated synthesis of nucleotide and nucleosides influenced by amino acids

Research on prebiotic chemistry and the origins of nucleic acids and proteins has traditionally been focussed on only one or the other. However, if nucleotides and amino acids co-existed on the early Earth, their mutual interactions and reactivity should be considered explicitly. Here we set out to investigate nucleotide/nucleoside formation by simple dehydration reactions of constituent building blocks (sugar, phosphate, and nucleobase) in the presence of different amino acids. We demonstrate the simultaneous formation of glycosidic bonds between ribose, purines, and pyrimidines under mild conditions without catalysts or activated reagents, as well as nucleobase exchange, in addition to the simultaneous formation of nucleotide and nucleoside isomers from several nucleobases. Clear differences in the distribution of glycosylation products are observed when glycine is present. This work demonstrates that reaction networks of nucleotides and amino acids should be considered when exploring the emergence of catalytic networks in the context of molecular evolution

CARB 113: Co-assembly of peptide and carbohydrate amphiphiles to generate proteoglycan mimics

Peptide amphiphiles (PA) have been used as building blocks that generate nanofibrous protein mimics through self-assembly under physiological conditions. These supramolecular structures are maintained by non-covalent interactions, such as, Pi-Pi stacking, hydrogen bonding and hydrophobic effects. The generated fibers can be further crosslinked via salt bridges thus forming hydrated systems that resemble the extracellular matrix (ECM) at structural and functional level. However, the proteins in the ECM are often presented as glycoconjugates such as glycoproteins and proteoglycans. Carbohydrate-modified PAs are just emerging as alternative or complementary building blocks able to generate closer supramolecular ECM mimics. Such PAs are challenging at synthetic, supramolecular and biofunctional level. Carbohydrates bear different â OH groups prompt to react and thus, different protections are needed for selective functionalization. Moreover, once conjugated to the PA, the carbohydrate moiety can alter its self-assembling capacity, as well as, the biofunctionality of the incorporated bioactive peptide. We therefore developed a simpler approach for generation of minimalistic proteoglycan mimics: co-assembly of short, aromatic PA and their carbohydrate analogues. The nanofibers generated by this approach have a PA core (e.g. fmoc-FF) and a carbohydrate shell (e.g. fmoc-glucosamine-6-phosphate or fmoc-glucosamine-6-sulfate). They present: 1) a higher mechanical performance than the PA single component systems; 2) an improved biofunctionality as demonstrated by our studies with growth factors (e.g. FGF2), lectins and cells. Peptide amphiphiles (PA) have been used as building blocks that generate nanofibrous protein mimics through self-assembly under physiological conditions. These supramolecular structures are maintained by non-covalent interactions, such as, Pi-Pi stacking, hydrogen bonding and hydrophobic effects. The generated fibers can be further crosslinked via salt bridges thus forming hydrated systems that resemble the extracellular matrix (ECM) at structural and functional level. However, the proteins in the ECM are often presented as glycoconjugates such as glycoproteins and proteoglycans. Carbohydrate-modified PAs are just emerging as alternative or complementary building blocks able to generate closer supramolecular ECM mimics. Such PAs are challenging at synthetic, supramolecular and biofunctional level. Carbohydrates bear different –OH groups prompt to react and thus, different protections are needed for selective functionalization. Moreover, once conjugated to the PA, the carbohydrate moiety can alter its self-assembling capacity, as well as, the biofunctionality of the incorporated bioactive peptide. We therefore developed a simpler approach for generation of minimalistic proteoglycan mimics: co-assembly of short, aromatic PA and their carbohydrate analogues. The nanofibers generated by this approach have a PA core (e.g. fmoc-FF) and a carbohydrate shell (e.g. fmoc-glucosamine-6-phosphate or fmoc-glucosamine-6-sulfate). They present: 1) a higher mechanical performance than the PA single component systems; 2) an improved biofunctionality as demonstrated by our studies with growth factors (e.g. FGF2), lectins and cells.  info:eu-repo/semantics/publishedVersio

Using evolutionary algorithms and machine learning to explore sequence space for the discovery of antimicrobial peptides

We present a proof-of-concept methodology for efficiently optimizing a chemical trait by using an artificial evolutionary workflow. We demonstrate this by optimizing the efficacy of antimicrobial peptides (AMPs). In particular, we used a closed-loop approach that combines a genetic algorithm, machine learning, and in vitro evaluation to improve the antimicrobial activity of peptides against Escherichia coli. Starting with a 13-mer natural AMP, we identified 44 highly potent peptides, achieving up to a ca. 160-fold increase in antimicrobial activity within just three rounds of experiments. During these experiments, the conformation of the peptides selected was changed from a random coil to an α-helical form. This strategy not only establishes the potential of in vitro molecule evolution using an algorithmic genetic system but also accelerates the discovery of antimicrobial peptides and other functional molecules within a relatively small number of experiments, allowing the exploration of broad sequence and structural space

Tunable supramolecular gel properties by varying thermal history

YesThe 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.FP7 Ideas: European Research Council. Grant Number: 25877

Biocatalytic self-assembly on magnetic nanoparticles

Combining (bio-)catalysis and molecular self-assembly provides an effective approach for the production and processing of self-assembled materials, by exploiting catalysis to direct the assembly kinetics and hence control the formation of ordered nanostructures. Applications of (bio-)catalytic self-assembly in biologically interfacing systems and in nanofabrication have recently been reported. Inspired by self-assembly in biological cells, efforts to confine catalysts on flat or patterned surfaces to exert spatial control over molecular gelator generation and nanostructure self-assembly have also emerged. Building on our previous work in the area, we demonstrate in this report the use of enzymes immobilized onto magnetic nanoparticles (NPs) to spatially localize the initiation of peptide self-assembly into nanofibers around NPs. The concept is generalized for both an equilibrium biocatalytic system that forms stable hydrogels and a non-equilibrium system that normally has a preset lifetime. Characterization of the hydrogels shows that self-assembly occurs at the site of enzyme immobilization on the NPs, to give rise to gels with a “hub-and-spoke” morphology where the nanofibers are linked through the enzyme-NP conjugates. This NP-controlled arrangement of self-assembled nanofibers enables remarkable enhancements in the shear strength of both hydrogel systems, as well as a dramatic extension of the hydrogel stability in the non-equilibrium system. We are also able to show that the use of magnetic NPs enables external control of both the formation of the hydrogel and its overall structure by application of an external magnetic field. We anticipate that the enhanced properties and stimuli-responsiveness of our NP-enzyme system will have applications ranging from nanomaterial fabrication to biomaterials and biosensing

Environmental control programs the emergence of distinct functional ensembles from unconstrained chemical reactions

Many approaches to the origin of life focus on how the molecules found in biology might be made in the absence of biological processes, from the simplest plausible starting materials. Another approach could be to view the emergence of the chemistry of biology as process whereby the environment effectively directs “primordial soups” toward structure, function, and genetic systems over time. This does not require the molecules found in biology today to be made initially, and leads to the hypothesis that environment can direct chemical soups toward order, and eventually living systems. Herein, we show how unconstrained condensation reactions can be steered by changes in the reaction environment, such as order of reactant addition, and addition of salts or minerals. Using omics techniques to survey the resulting chemical ensembles we demonstrate there are distinct, significant, and reproducible differences between the product mixtures. Furthermore, we observe that these differences in composition have consequences, manifested in clearly different structural and functional properties. We demonstrate that simple variations in environmental parameters lead to differentiation of distinct chemical ensembles from both amino acid mixtures and a primordial soup model. We show that the synthetic complexity emerging from such unconstrained reactions is not as intractable as often suggested, when viewed through a chemically agnostic lens. An open approach to complexity can generate compositional, structural, and functional diversity from fixed sets of simple starting materials, suggesting that differentiation of chemical ensembles can occur in the wider environment without the need for biological machinery

Alignment of nanostructured tripeptide gels by directional ultrasonication

We demonstrate an in-situ ultrasonic approach to influence self-assembly across the supramolecular to micron length scales, showing enhancement of supramolecular interactions, chirality and orientation, which depends on the peptide sequence and solvent environment. This is the first successful demonstration of using oscillating pressure waves to generate anisotropic organo- and hydro- gels consisting of oriented tripeptides structures