Sequenced defined biomolecules for nanomaterial synthesis, functionalization, and assembly

Energies Exploration for the Troponine Molecule Supported on Carbon Nanomaterials: DFT Study

Density functional theory calculations have been used to elucidate structural parameters of pristine cardiac Troponin I and its interaction with carbon nanomaterials. In this case, zigzag single-walled carbon nanotubes and graphene sheets were selected. Troponin I interacted horizontally (leusine terminal) and vertically (lysine terminal) with the nanomaterials. Cohesion and binding energies, band gaps, and charge transfer for the systems were obtained. Cohesion for troponin I supported on graphene and single-walled carbon nanotube in the horizontal position was found to be the most viable system. Binding for the interaction between troponin I and a nanotube in the horizontal position was found to be the most stable with a value of 0.002 eV that increases to 0.004 eV with a van der Waals correction. Furthermore, the density of states exhibits an improvement in band gap for graphene sheets, and finally, a higher charge transfer was reported for troponin I in its horizontal form supported on a zigzag single-walled carbon nanotube.

Mariz B, Moreira IP, Kalafatovic D, Morais Faustino BM, Narang V, Wang T, Pappas CG, Ferreira I, Roque ACA, Ulijn RV. Discovery of phosphotyrosine-binding oligopeptides with supramolecular target selectivity

Phage-display screening on self-assembled tyrosine-phosphate ligands enables the identification of oligopeptides selective to dynamic supramolecular targets, with the lead peptide showing a preferred hairpin-like conformation and catalytic activity.

Synthesis and Processing of Nanomaterials Mediated by Living Organisms

Nanomaterials offer exciting properties and functionalities. However, their production and processing frequently involve complex methods, cumbersome equipment, harsh conditions, and hazardous media. The capability of organisms to accomplish this using mild conditions offers a sustainable, biocompatible, and environmentally friendly alternative. Different nanomaterials such as metal nanoparticles, quantum dots, silica nanostructures, and nanocellulose are being synthesized increasingly through living entities. In addition, the bionanofabrication potential enables also the in situ processing of nanomaterials inside biomatrices with unprecedented outcomes. In this Minireview we present a critical state‐of‐the‐art vision of current nanofabrication approaches mediated by living entities (ranging from unicellular to higher organisms), in order to expand this knowledge and scrutinize future prospects. An efficient interfacial interaction at the nanoscale by green means is within reach through this approach.

Exploiting Peptide Self-Assembly for the Development of Minimalistic Viral Mimetics

Viruses are natural supramolecular nanostructures that form spontaneously by molecular self-assembly of complex biomolecules. Peptide self-assembly is a versatile tool that allows mimicking viruses by creating their simplified versions through the design of functional, supramolecular materials with modularity, tunability, and responsiveness to chemical and physical stimuli. The main challenge in the design and fabrication of peptide materials is related to the precise control between the peptide sequence and its resulting supramolecular morphology. We provide an overview of existing sequence patterns employed for the development of spherical and fibrillar peptide assemblies that can act as viral mimetics, offering the opportunity to tackle the challenges of viral infections.

Peptide-Engineered Fluorescent Nanomaterials: Structure Design, Function Tailoring, and Biomedical Applications

Fluorescent nanomaterials have exhibited promising applications in biomedical and tissue engineering fields. To improve the properties and expand bioapplications of fluorescent nanomaterials, various functionalization and biomodification strategies have been utilized to engineer the structure and function of fluorescent nanomaterials. Due to their high biocompatibility, satisfied bioactivity, unique biomimetic function, easy structural tailoring, and controlled self-assembly ability, supramolecular peptides are widely used as versatile modification agents and nanoscale building blocks for engineering fluorescent nanomaterials. In this work, recent advance in the synthesis, structure, function, and biomedical applications of peptide-engineered fluorescent nanomaterials is presented. Firstly, the types of different fluorescent nanomaterials are introduced. Then, potential strategies for the preparation of peptide-engineered fluorescent nanomaterials via templated synthesis, bioinspired conjugation, and peptide assembly-assisted synthesis are discussed. After that, the unique structure and functions through the peptide conjugation with fluorescent nanomaterials are demonstrated. Finally, the biomedical applications of peptide-engineered fluorescent nanomaterials in bioimaging, disease diagnostics and therapy, drug delivery, tissue engineering, antimicrobial test, and biosensing are presented and discussed in detail. It is helpful for readers to understand the peptide-based conjugation and bioinspired synthesis of fluorescent nanomaterials, and to design and synthesize novel hybrid bionanomaterials with special structures and improved functions for advanced applications.

Electrochemical Determination of Nicotine in Tobacco Products Based on Biosynthesized Gold Nanoparticles

In this work, gold nanoparticles were biosynthesized via Plectranthus amboinicus leaf extract as the reducing agent. A series of techniques were used for sample analysis. The biosynthesized gold nanoparticles (bAuNPs) are a uniform size with a spherical shape. The FTIR analysis reveals the presence of many oxygen-containing functional groups on the bAuNP surface. The cyclic voltammetry and electrochemical impedance spectroscopic characterizations reveal that while the bAuNPs have a slightly lower conductivity than chemically synthesized AuNPs (cAuNPs). However, the bAuNPs have a superior electrocatalytic performance toward nicotine reduction. After optimization, the bAuNP-modified SPE could detect nicotine linearly from 10 to 2,000 μM with a low detection limit of 2.33 μM. In addition, the bAuNPs/SPE have been successfully used for nicotine-containing-product analysis.

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.

Energy Landscapes of a Pair of Adsorbed Peptides

The wide relevance of peptide adsorption in natural and synthetic contexts means it has attracted much attention. Molecular dynamics (MD) simulation has been widely used in these endeavors. Much of this has focused on single peptides due to the computational effort required to capture the rare events that characterize their adsorption. This focus is, however, of limited practical relevance as in reality, most systems of interest operate in the nondilute regime where peptides will interact with other adsorbed peptides. As an alternative to MD simulation, we have used energy landscape mapping (ELM) to investigate two met-enkephalin molecules adsorbed at a gas/graphite interface. Major conformations of the adsorbed peptides and the connecting transition states are elucidated along with the associated energy barriers and rates of exchange. The last of these makes clear that MD simulations are currently of limited use in probing the co-adsorption of two peptides, let alone more. The constant volume heat capacity as a function of temperature is also presented. Overall, this study represents a significant step toward characterizing peptide adsorption beyond the dilute limit.

Chiral Restructuring of Peptide Enantiomers on Gold Nanomaterials

The use of biomolecules has been invaluable at generating and controlling optical chirality in nanomaterials; however, the structure and properties of the chiral biotemplate are not well understood due to the complexity of peptide-nanoparticle interactions. In this study, we show that the complex interactions between d-peptides and gold nanomaterials led to a chiral restructuring of peptides as demonstrated by circular dichroism and proteolytic cleavage of d-peptides via gold-mediated inversion of peptide chirality. The gold nanoparticles synthesized using d-peptide produce a highly ordered atomic surface and restructured peptide bonds for enzyme cleavage. Differences in gold nanoparticle catalyzed reduction of 4-nitrophenol were observed on the basis of the chiral peptide used in nanoparticle synthesis. Notably, the proteolytic cleavage of d-peptides on gold provides an opportunity for designing nanoparticle based therapeutics to treat peptide venoms, access new chemistries, or modulate the catalytic activity of nanomaterials.

Anisotropic Gold Nanoparticle-Cell Interactions Mediated by Collagen

Gold nanoparticles (AuNPs) are the groundwork of a large variety of applications in the biomedical field. Further development and a better understanding of this versatile platform will lead to an expansion of potential applications. In this study, we propose a facile synthesis of AuNPs using hydrogen peroxide as a reducing agent and collagen as a stabilizing agent. Our synthetic approach results in "raspberry"-like AuNPs with a mean diameter of 60 nm, as revealed by electron microscopy. The optical properties of the AuNPs were assessed by UV-Vis and surface-enhanced Raman scattering (SERS), and their stability and in vitro cytotoxicity were evaluated as well. HeLa cell viability values were only modestly affected compared to control, with the highest concentration tested displaying a 20% decrease in cellular viability. The dose-dependent cellular internalization in the 20⁻60 nM range indicate the highest internalization rate at 60 nM and uptake values as high as 35%. This result correlated well with the viability results. These type of anisotropic AuNPs are proposed for biomedical applications such as hyperthermia, contrast agents or imaging. Therefore, our findings offer a platform for potential biological applications such as sensing and imaging, due to their unique physico-chemical features.

Tyrosine-Rich Peptides as a Platform for Assembly and Material Synthesis

The self-assembly of biomolecules can provide a new approach for the design of functional systems with a diverse range of hierarchical nanoarchitectures and atomically defined structures. In this regard, peptides, particularly short peptides, are attractive building blocks because of their ease of establishing structure-property relationships, their productive synthesis, and the possibility of their hybridization with other motifs. Several assembling peptides, such as ionic-complementary peptides, cyclic peptides, peptide amphiphiles, the Fmoc-peptide, and aromatic dipeptides, are widely studied. Recently, studies on material synthesis and the application of tyrosine-rich short peptide-based systems have demonstrated that tyrosine units serve as not only excellent assembly motifs but also multifunctional templates. Tyrosine has a phenolic functional group that contributes to π-π interactions for conformation control and efficient charge transport by proton-coupled electron-transfer reactions in natural systems. Here, the critical roles of the tyrosine motif with respect to its electrochemical, chemical, and structural properties are discussed and recent discoveries and advances made in tyrosine-rich short peptide systems from self-assembled structures to peptide/inorganic hybrid materials are highlighted. A brief account of the opportunities in design optimization and the applications of tyrosine peptide-based biomimetic materials is included.

Interactions between Metal Oxides and Biomolecules: from Fundamental Understanding to Applications

Metallo-oxide (MO)-based bioinorganic nanocomposites promise unique structures, physicochemical properties, and novel biochemical functionalities, and within the past decade, investment in research on materials such as ZnO, TiO₂, SiO₂, and GeO₂ has significantly increased. Besides traditional approaches, the synthesis, shaping, structural patterning, and postprocessing chemical functionalization of the materials surface is inspired by strategies which mimic processes in nature. Would such materials deliver new technologies? Answering this question requires the merging of historical knowledge and current research from different fields of science. Practically, we need an effective defragmentation of the research area. From our perspective, the superficial accounting of material properties, chemistry of the surfaces, and the behavior of biomolecules next to such surfaces is a problem. This is particularly of concern when we wish to bridge between technologies in vitro and biotechnologies in vivo. Further, besides the potential practical technological efficiency and advantages such materials might exhibit, we have to consider the wider long-term implications of material stability and toxicity. In this contribution, we present a critical review of recent advances in the chemistry and engineering of MO-based biocomposites, highlighting the role of interactions at the interface and the techniques by which these can be studied. At the end of the article, we outline the challenges which hamper progress in research and extrapolate to developing and promising directions including additive manufacturing and synthetic biology that could benefit from molecular level understanding of interactions occurring between inanimate (abiotic) and living (biotic) materials.

Controlled synthesis of highly-branched plasmonic gold nanoparticles through peptoid engineering

In nature, specific biomolecules interacting with mineral precursors are responsible for the precise production of nanostructured inorganic materials that exhibit complex morphologies and superior performance. Despite advances in developing biomimetic approaches, the design rules for creating sequence-defined molecules that lead to the synthesis of inorganic nanomaterials with predictable complex morphologies are unknown. Herein we report the design of sequence-defined peptoids for controlled synthesis of highly branched plasmonic gold particles. By engineering peptoid sequences and investigating the resulting particle formation mechanisms, we develop a rule of thumb for designing peptoids that predictively enabled the morphological evolution from spherical to coral-shaped nanoparticles. Through a combination of hyperspectral UV-Vis extinction microscopy and three-photon photoemission electron microscopy, we demonstrate that the individual coral-shaped gold nanoparticles exhibit a plasmonic enhancement as high as 10⁵-fold. This research significantly advances our ultimate vision of predictive bio-inspired materials synthesis using sequence-defined synthetic molecules that mimic proteins and peptides.

Peptoids are promising crystallization agents, as they offer the molecular recognition capabilities of proteins and peptides but with higher stability and synthetic tunability. Here, the authors show that sequence-defined peptoids can controllably template the formation and shape evolution of gold nanostructures with defined morphologies.

Hemoglobin-driven iron-directed assembly of gold nanoparticles

The ability to form complex 3D architectures using nanoparticles (NPs) as the building blocks and complex macromolecules that direct these assemblies remains a challenging objective for nanotechnology. Here we report results in which the partial substitution of classical Turkevich citrate-capped gold NPs by a novel, heteroaromatic ligand (L) results in NPs able to form coordination-driven assemblies mediated by free or protein-bound iron ions. The morphology of these assemblies can be tuned depending on the source of iron. To prove the concept, classical citrate and novel NPs were reacted with iron-containing protein hemoglobin (Hb). To diminish the influence of possible electrostatic interactions of native Hb and gold NPs, the reaction was performed at the isoelectric point of Hb. Moreover, thiol groups of Hb were protected with p-quinone to exclude thiol–gold bond formation. As expected, citrate-capped gold NPs are well dispersed in functionalized Hb, while L-functionalized NPs form assemblies. The blue shift of the Soret band of the functionalized Hb, when reacted with novel NPs, unambiguously confirms the coordination of a NP-anchored heteroaromatic ligand with the heme moiety of Hb. Coarse-grained molecular dynamics of this system were performed to gain information about aggregation dynamics and kinetics of iron- and hemoglobin-templated assemblies of L–NPs. A multi-scale simulation approach was employed to extend this model to longer time scales. The application of this model towards novel coordination-based assemblies can become a powerful tool for the development of new nanomaterials.

The ability to form complex 3D architectures using nanoparticles as the building blocks and complex macromolecules that direct these assemblies remains a challenging objective for nanotechnology.