Peptide Integrated Optics

Detection of helical water flows in sub-nanometer channels

Nanoscale flows of liquids can be revealed in various biological processes and underlie a wide range of nanofluidic applications. Though the integral characteristics of these systems, such as permeability and effective diffusion coefficient, can be measured in experiments, the behaviour of the flows within nanochannels is still a matter of speculation. Herein, we used a combination of quadrupolar solid-state NMR spectroscopy, computer simulation, and dynamic vapour sorption measurements to analyse water diffusion inside peptide nanochannels. We detected a helical water flow coexisting with a conventional axial flow that are independent of each other, immiscible, and associated with diffusion coefficients that may differ up to 3 orders of magnitude. The trajectory of the helical flow is dictated by the screw-like distribution of ionic groups within the channel walls, while its flux is governed by external water vapour pressure. Similar flows may occur in other types of nanochannels containing helicoidally distributed ionic groups and be exploited in various nanofluidic lab-on-a-chip devices.

A Comprehensive Analysis of the Intrinsic Visible Fluorescence Emitted by Peptide/Protein Amyloid-like Assemblies

Amyloid aggregation is a widespread process that involves proteins and peptides with different molecular complexity and amino acid composition. The structural motif (cross-β) underlying this supramolecular organization generates aggregates endowed with special mechanical and spectroscopic properties with huge implications in biomedical and technological fields, including emerging precision medicine. The puzzling ability of these assemblies to emit intrinsic and label-free fluorescence in regions of the electromagnetic spectrum, such as visible and even infrared, usually considered to be forbidden in the polypeptide chain, has attracted interest for its many implications in both basic and applied science. Despite the interest in this phenomenon, the physical basis of its origin is still poorly understood. To gain a global view of the available information on this phenomenon, we here provide an exhaustive survey of the current literature in which original data on this fluorescence have been reported. The emitting systems have been classified in terms of their molecular complexity, amino acid composition, and physical state. Information about the wavelength of the radiation used for the excitation as well as the emission range/peak has also been retrieved. The data collected here provide a picture of the complexity of this multifaceted phenomenon that could be helpful for future studies aimed at defining its structural and electronic basis and/or stimulating new applications.

Fmoc-diphenylalanine gelating nanoarchitectonics: A simplistic peptide self-assembly to meet complex applications

9-fluorenylmethoxycarbonyl-diphenylalanine (Fmoc-FF), has been has been extensively explored due to its ultrafast self-assembly kinetics, inherent biocompatibility, tunable physicochemical properties, and especially, the capability of forming self-sustained gels under physiological conditions. Consequently, various methodologies to develop Fmoc-FF gels and their corresponding applications in biomedical and industrial fields have been extensively studied. Herein, we systemically summarize the mechanisms underlying Fmoc-FF self-assembly, discuss the preparation methodologies of Fmoc-FF hydrogels, and then deliberate the properties as well as the diverse applications of Fmoc-FF self-assemblies. Finally, the contemporary shortcomings which limit the development of Fmoc-FF self-assembly are raised and the alternative solutions are proposed, along with future research perspectives.

A Robust Ratiometric Fluorescent Sensor Based on Covalent Assembly of Dipeptides and Biomolecules for the High-Sensitive and Optosmart Detection of Pyrethroids

In this study, two ultrashort dipeptides, diphenylalanine (FF) or C-terminal amidated diphenylalanine (DPA), were covalently self-assembled with genipin to obtain two well-defined supramolecular peptide nanoparticles for the detection of pyrethroids. DPA-genipin nanoparticles (PNPs) demonstrated excellent dual-emission fluorescence characteristics, tunable particle size, and robust photostability. Parallel to this, PNPs showed a ratiometric fluorescence response to λ-cyhalothrin (LC) with a distinct green-to-red color transition. The satisfactory self-calibration capability of the ratiometric system enabled PNPs to respond sensitively to LC in a wide range (5-800 μg/L) with a lower limit of detection of 0.034 μg/L. The introduction of a smartphone application made it easy to develop an intelligent evaluation platform based on PNPs, which had been proven to be applicable for on-site visualization of LC in agricultural products. The platform proposed here may be a new application of peptide self-assembly in sensing, with both important food safety implications and great economic value.

Switchable Ultra-Wideband All-Optical Quantum Dot Reflective Semiconductor Optical Amplifier

A comprehensive study has been conducted on ultra-broadband optically pumped quantum dot (QD) reflective semiconductor optical amplifiers (QD-RSOAs). Furthermore, little work has been done on broadband QD-RSOAs with an optical pump. About 1 μm optical bandwidth, spanning 800 nm up to 1800 nm, is supported for the suggested device by superimposing nine groups of QDs. It has been shown that the device can be engineered to amplify a selected window or a group of desired windows. Moreover, the operation of the device has been thoroughly investigated by solving the coupled differential rate and signal propagation equations. A numerical algorithm has been suggested to solve these equations. As far as we are concerned, a broadband optically pumped QD-RSOA that can operate as a filter has been introduced.

Non-Conventional Peptide Self-Assembly into a Conductive Supramolecular Rope

Structures composed of alternating α and β amino acids can give rise to peculiar secondary structural motifs, which could self-assemble into complex structures of controlled geometries. This work describes the self-assembly properties of an α,β-peptide, containing three units of syn H2-(2-F-Phe)-h-PheGly-OH, able to self-organize on surfaces into a fascinating supramolecular rope. This material was characterized by AFM, electronic conduction and fluorescence measurements. Molecular dynamics simulations showed that this hexapeptide can self-assemble into an antiparallel β-sheet layer, stabilized by intermolecular H-bonds, which, in turn, can self-assemble into many side-by-side layers, due to π-π interactions. As a matter of fact, we demonstrated that in this system, the presence of aromatic residues at the intramolecular interface promoted by the alternation of α,β-amino-acids in the primary sequence, endorses the formation of a super-secondary structure where the aromatic groups are close to each other, conferring to the system good electron conduction properties. This work demonstrates the capability and future potential of designing and fabricating distinctive nanostructures and efficient bioelectronic interfaces based on an α,β-peptide, by controlling structure and interaction processes beyond those obtained with α- or β-peptides alone.

Three-Dimensional Printing of Dipeptides with Spatioselective Programming of Crystallinity for Multilevel Anticounterfeiting

The functionalities of peptide microstructures and nanostructures can be enhanced by controlling their crystallinity. Gaining control over the crystallinity within the desired structure, however, remains a challenge. We have developed a three-dimensional (3D) printing method that enables spatioselective programming of the crystallinity of diphenylalanine (FF) dipeptide microarchitectures. A femtoliter ink meniscus is used to spatially control reprecipitation self-assembly, enabling the printing of a freestanding FF microstructure with programmed shape and crystallinity. The self-assembly crystallization of FF can be switched on and off at will by controlling the evaporation of the binary solvent. The evaporation-dependent crystallization was theoretically studied by the numerical simulation of supersaturation fields in the meniscus. We found that a 3D-printed FF microarchitecture with spatially programmed crystallinity can carry a 3D digital optical anisotropy pattern, applicable to generating polarization-encoded anticounterfeiting labels. This crystallinity-controlled additive manufacturing will pave the new way for facilitating the creation of peptide-based devices.

Non-Aromatic Fluorescence in Biological Matter: The Exception or the Rule?

While in the vast majority of cases fluorescence in biological matter has been attributed to aromatic or conjugated groups, peptides associated with neurodegenerative diseases, such as Alzheimer's, Parkinson's, or Huntington's, have been recently shown to display an intrinsic visible fluorescence even in the absence of aromatic residues. This has called the attention of researchers from many different fields, trying to understand the origin of this peculiar behavior and, at the same time, motivating the search for novel strategies to control the optical properties of new biophotonic materials. Today, after nearly 15 years of its discovery, there is a growing consensus about the mechanism underlying this phenomenon, namely, that electronic interactions between non-optically active molecules can result in supramolecular assemblies that are fluorescent. Despite this progress, many aspects of this phenomenon remain uncharted territory. In this Perspective, we lay down the state-of-the-art in the field highlighting the open questions from both experimental and theoretical fronts in this fascinating emerging area of non-aromatic fluorescence.

Gentle Patterning Approaches toward Compatibility with Bio-Organic Materials and Their Environmental Aspects

Advances in material science, bioelectronic, and implantable medicine combined with recent requests for eco-friendly materials and technologies inevitably formulate new challenges for nano- and micropatterning techniques. Overall, the importance of creating micro- and nanostructures is motivated by a large manifold of fundamental and applied properties accessible only at the nanoscale. Lithography is a crucial family of fabrication methods to create prototypes and produce devices on an industrial scale. The pure trend in the miniaturization of critical electronic semiconducting components has been recently enhanced by implementing bio-organic systems in electronics. So far, significant efforts have been made to find novel lithographic approaches and develop old ones to reach compatibility with delicate bio-organic systems and minimize the impact on the environment. Herein, such delicate materials and sophisticated patterning techniques are briefly reviewed.

A Computational Approach to Nontraditional Intrinsic Luminescence: Vibrationally Resolved Absorption and Fluorescence Spectra of DABCO

Recently, so-called "nontraditional intrinsic luminescence" has been reported in several macromolecular systems. Although DABCO (1,4-diazabicyclo[2.2.2]octane) is the first system in which the effect was observed, a thorough analysis of the optical properties of the molecule, which would reveal the origin of this mysterious effect, is still pending. We perform an advanced post-Hartree-Fock treatment of the low-lying electronic states of this molecule, which need to be described with care because of their pronounced Rydberg character. We take a deeper look into the low-lying electronic transitions of DABCO targeting the explanation of the complex vibronic structures of its absorption and fluorescence spectra. Two electronic states, the ¹E'(n₊3p_xy) and ¹A₂^″(n₊3p_z) states, contribute to the absorption spectrum in the 39000-46000 cm^-1 spectral range. We also reveal the spectroscopic signature of the ¹A₂^″(n₊3p_z) state. The analyses of the contributions of individual vibrational normal modes allowed the identification of those giving rise to the complex vibronic structures of the spectra. Fluorescence emission arises from the vibronic coupling of the one-photon forbidden transition between the ¹A₁^'(n₊3s) state and the electronic ground state. The spectrum, which can be interpreted in terms of populating a few vibrational normal modes, is shifted toward visible wavelengths mostly due to the forced interaction of the lone pair electrons of the two nitrogen atoms. Our work on DABCO may help to rationalize the luminescence of more complex systems containing tertiary amine groups.

Peptide Coassembly to Enhance Piezoelectricity for Energy Harvesting

The discovery of piezoelectricity in self-assembled peptide nanostructures opens an avenue to a new regime of piezoelectric materials and enables the fundamental investigation of electromechanical coupling in biomaterials. However, strategies for fabricating peptides with desired properties are still lacking. We find that a peptide-based coassembly process effectively controls the properties of peptide nanomaterials and demonstrates their application potential in nanogenerators. The composing peptides and their concentration influence the morphology, molecular property, and physical property of coassembled crystals. Compared with self-assembled diphenylalanine peptides, the coassembled peptides of diphenylalanine and phenylalanine-tryptophan show a 38% increase in piezoelectric coefficient, and the resulting harvesting device shows nearly a 3-fold increase in open-circuit voltage outputs.

Amyloid-like Prep1 peptides exhibit reversible blue-green-red fluorescence in vitro and in living cells

PREP1-based peptides form amyloid-like aggregates endowed with an intrinsic blue-green-red fluorescence with an unusual sharp maximum at 520 nm upon excitation with visible light under physiological conditions. The peptide PREP1[117-132], whose sequence does not contain aromatic residues, presents a pH-dependent and reversible fluorescence, in line with its structural transition from β-sheet rich aggregates to α-helix structures. These findings further demonstrate that the non-canonical fluorescence exhibited by amyloids is an articulated phenomenon.

Peptide-based hydrogels as delivery systems for doxorubicin

Hydrogels (HGs) and nanogels (NGs) have been recently identified as innovative supramolecular materials for many applications in biomedical field such as in tissue engineering, optoelectronic, and local delivery of active pharmaceutical ingredients (APIs). Due to their in vivo biocompatibility, synthetic accessibility, low cost, and tunability, peptides have been used as suitable building blocks for preparation of HGs and NGs formulations. Peptide HGs have shown an outstanding potential to deliver small drugs, protein therapeutics, or diagnostic probes, maintaining the efficacy of their loaded molecules, preventing degradation phenomena, and responding to external physicochemical stimuli. In this review, we discuss the possible use of peptide-based HGs and NGs as vehicles for the delivery of the anticancer drug doxorubicin (Dox). This anthracycline is clinically used for leukemia, stomach, lung, ovarian, breast, and bladder cancer therapy. The loading of Dox into supramolecular systems (liposomes, micelles, hydrogels, and nanogels) allows reducing its cardiotoxicity. According to a primary sequence classification of the constituent peptide, doxorubicin-loaded systems are here classified in short and ultra-short peptide-based HGs, RGD, or RADA-peptide-based HGs and peptide-based NGs.

Controlling the Formation of Peptide Films: Fully Developed Helical Peptides are Required to Obtain a Homogenous Coating over a Large Area

The influence of conformational dynamics on the self-assembly process of a conformationally constrained analogue of the natural antimicrobial peptide Trichogin GA IV was analysed by spectroscopic methods, microscopy imaging at nanometre resolution, and molecular dynamics simulations. The formation of peptide films at the air/water interface and their deposition on a graphite or a mica substrate were investigated. A combination of experimental evidence with molecular dynamics simulation was used to demonstrate that only the fully developed helical structure of the analogue promotes formation of ordered aggregates that nucleate the growth of micrometric rods, which give rise to homogenous coating over wide regions of the hydrophilic mica. This work proves the influence of helix flexibility on peptide self-organization and orientation on surfaces, key steps in the design of bioinspired organic/inorganic hybrid materials.

Fluorescence Phenomena in Amyloid and Amyloidogenic Bionanostructures

Nanoscale optical labeling is an advanced bioimaging tool. It is mostly based on fluorescence (FL) phenomena and enables the visualization of single biocells, bacteria, viruses, and biological tissues, providing monitoring of functional biosystems in vitro and in vivo, and the imaging-guided transportation of drug molecules. There is a variety of FL biolabels such as organic molecular dyes, genetically encoded fluorescent proteins (green fluorescent protein and homologs), semiconductor quantum dots, carbon dots, plasmonic metal gold-based nanostructures and more. In this review, a new generation of FL biolabels based on the recently found biophotonic effects of visible FL are described. This intrinsic FL phenomenon is observed in any peptide/protein materials folded into β-sheet secondary structures, irrespective of their composition, complexity, and origin. The FL effect has been observed both in natural amyloid fibrils, associated with neurodegenerative diseases (Alzheimer’s, Parkinson’s, and more), and diverse synthetic peptide/protein structures subjected to thermally induced biological refolding helix-like→β-sheet. This approach allowed us to develop a new generation of FL peptide/protein bionanodots radiating multicolor, tunable, visible FL, covering the entire visible spectrum in the range of 400–700 nm. Newly developed biocompatible nanoscale biomarkers are considered as a promising tool for emerging precise biomedicine and advanced medical nanotechnologies (high-resolution bioimaging, light diagnostics, therapy, optogenetics, and health monitoring).

Biopolymeric photonic structures: design, fabrication, and emerging applications

Biological photonic structures can precisely control light propagation, scattering, and emission via hierarchical structures and diverse chemistry, enabling biophotonic applications for transparency, camouflaging, protection, mimicking and signaling. Corresponding natural polymers are promising building blocks for constructing synthetic multifunctional photonic structures owing to their renewability, biocompatibility, mechanical robustness, ambient processing conditions, and diverse surface chemistry. In this review, we provide a summary of the light phenomena in biophotonic structures found in nature, the selection of corresponding biopolymers for synthetic photonic structures, the fabrication strategies for flexible photonics, and corresponding emerging photonic-related applications. We introduce various photonic structures, including multi-layered, opal, and chiral structures, as well as photonic networks in contrast to traditionally considered light absorption and structural photonics. Next, we summarize the bottom-up and top-down fabrication approaches and physical properties of organized biopolymers and highlight the advantages of biopolymers as building blocks for realizing unique bioenabled photonic structures. Furthermore, we consider the integration of synthetic optically active nanocomponents into organized hierarchical biopolymer frameworks for added optical functionalities, such as enhanced iridescence and chiral photoluminescence. Finally, we present an outlook on current trends in biophotonic materials design and fabrication, including current issues, critical needs, as well as promising emerging photonic applications.

Light waveguiding in bioinspired peptide nanostructures

Basic optical properties of bioinspired peptide nanostructures are deeply modified by thermally mediated refolding of peptide secondary structure from α-helical to β-sheet. This conformational transition is followed by the appearance in the β-sheet structures of a wideband optical absorption and fluorescence in the visible region. We demonstrate that a new biophotonic effect of optical waveguiding recently observed in peptide/protein nanoensembles is a structure-sensitive bimodal phenomenon. In the primary α-helical structure input, light propagates via optical transmission window demonstrating conventional passive waveguiding, based on classical optics. In the β-sheet structure, fluorescent (active) light waveguiding is revealed. The latter can be attributed to completely different physical mechanism of exciton-polariton propagation, characterized by high effective refractive index, and can be observed in nanoscale fibers below diffraction limit. It has been shown that peptide material requirements for passive and active waveguiding are dissimilar. Original biocompatibility and biodegradability indicate high potential future applications of these bioinspired waveguiding materials in precise photobiomedicine towards advanced highly selective bioimaging, photon diagnostics, and optogenetics.

Peptide Nanophotonics: From Optical Waveguiding to Precise Medicine and Multifunctional Biochips

Optical waveguiding phenomena found in bioinspired chemically synthesized peptide nanostructures are a new paradigm which can revolutionize emerging fields of precise medicine and health monitoring. A unique combination of their intrinsic biocompatibility with remarkable multifunctional optical properties and developed nanotechnology of large peptide wafers makes them highly promising for new biomedical light therapy tools and implantable optical biochips. This Review highlights a new field of peptide nanophotonics. It covers peptide nanotechnology and the fabrication process of peptide integrated optical circuits, basic studies of linear and nonlinear optical phenomena in biological and bioinspired nanostructures, and their passive and active optical waveguiding. It is shown that the optical properties of this generation of bio-optical materials are governed by fundamental biological processes. Refolding the peptide secondary structure is followed by wideband optical absorption and visible tunable fluorescence. In peptide optical waveguides, such a bio-optical effect leads to switching from passive waveguiding mode in native α-helical phase to an active one in the β-sheet phase. The found active waveguiding effect in β-sheet fiber structures below optical diffraction limit opens an avenue for the future development of new bionanophotonics in ultrathin peptide/protein fibrillar structures toward advanced biomedical nanotechnology.