'Wild Type'.

In this opinion piece, we consider the meaning of the term 'wild type' in the context of microbiology. This is especially pertinent in the post-genomic era, where we have a greater awareness of species diversity than ever before. Genomic heterogeneity, in vitro evolution/selection pressures, definition of 'the wild', the size and importance of the pan-genome, gene-gene interactions (epistasis), and the nature of the 'wild-type gene' are all discussed. We conclude that wild type is an outdated and even misleading phrase that should be gradually phased out.

Antiviral Activity of Peptide-Based Assemblies.

The COVID-19 pandemic highlighted the importance of developing surfaces and coatings with antiviral activity. Here, we present, for the first time, peptide-based assemblies that can kill viruses. The minimal inhibitory concentration (MIC) of the assemblies is in the range tens of micrograms per milliliter. This value is 2 orders of magnitude smaller than the MIC of metal nanoparticles. When applied on a surface, by drop casting, the peptide spherical assemblies adhere to the surface and form an antiviral coating against both RNA- and DNA-based viruses including coronavirus. Our results show that the coating reduced the number of T4 bacteriophages (DNA-based virus) by 3 log, compared with an untreated surface and 6 log, when compared with a stock solution. Importantly, we showed that this coating completely inactivated canine coronavirus (RNA-based virus). This peptide-based coating can be useful wherever sterile surfaces are needed to reduce the risk of viral transmission.

Non-covalently embedded oxytocin in alkanethiol monolayer as Zn2+ selective biosensor.

Peptides are commonly used as biosensors for analytes such as metal ions as they have natural binding preferences. In our previous peptide-based impedimetric metal ion biosensors, a monolayer of the peptide was anchored covalently to the electrode. Binding of metal ions resulted in a conformational change of the oxytocin peptide in the monolayer, which was measured using electrochemical impedance spectroscopy. Here, we demonstrate that sensing can be achieved also when the oxytocin is non-covalently integrated into an alkanethiol host monolayer. We show that ion-binding cause morphological changes to the dense host layer, which translates into enhanced impedimetric signals compared to direct covalent assembly strategies. This biosensor proved selective and sensitive for Zn2+ ions in the range of nano- to micro-molar concentrations. This strategy offers an approach to utilize peptide flexibility in monitoring their response to the environment while embedded in a hydrophobic monolayer.

Structural preferences of an anti-fouling peptide: From single chain to small molecular assemblies.

The structural features of a tripeptide constituted by two different non-coded amino acids, 3,4-dihydroxy-L-phenylalanine (L-DOPA) and 4-fluoro-Phenylalanine, (Phe(4F)), have been investigated by means of classical mechanics simulations. This tripeptide had been characterised as an antifouling agent with great adhesion capabilities. In this work, its conformational preferences have been described in two different environments (gas phase and water solution), at three different pHs and with different degrees of terminal capping. At the same time, the structural dynamics of small aggregates of the tripeptide have been investigated and their ability to stabilise ß-sheet based assemblies has been studied. The reported results describe the complexity of the tripeptide conformational preferences due to both the amphiphilic nature of its side chains, and the effect of the ionisation state resulting from the solution conditions. The investigations performed with small tripeptide assemblies in water solution reproduced the previously reported structural features, such as the polymorphism of its aggregates as a function of the pH. At edge pH values, the electrostatic screening imposed by the ions present in the solution facilitates the aggregation of the tripeptide chains, while at neutral pH and low concentrations of ionised species, the polar groups and the hydrogen bond capable groups impose their strength and lead to the disaggregation of the peptide clusters by favouring the solvation of individual chains rather than stabilising the aggregated states.

Amphiphilic Peptide with Dual Functionality Resists Biofouling.

Biofouling, the accumulation of organisms on surfaces, can lead to several undesirable phenomena, including hospital-acquired infections, blockage of water purification systems, and food contamination. The solution to the problem should be nontoxic and environmentally friendly, so that it could be applied on different surfaces and could come into contact with food, water, or human tissues. Peptides can provide such a solution, since they are biocompatible and biodegradable materials that can resist biofouling, either by preventing the attachment of organisms to the surface (antifouling) or by killing the bacteria (antimicrobial activity). This paper presents an amphiphilic peptide with antifouling, antimicrobial, and adhesive properties. The peptide adheres to titanium surfaces and inhibits the adhesion of both Gram-negative and Gram-positive bacteria to surfaces. In addition, it reduces the growth of bacteria in solution. This peptide has both antifouling and antimicrobial properties, which could be useful in health care systems, food packaging, and other systems that suffer from biocontamination.

Preventing Biofilm Formation by Dairy-Associated Bacteria Using Peptide-Coated Surfaces.

Biofilm-forming bacteria, which colonize the surfaces of equipment in the dairy industry, may adversely affect the safety and quality of the milk and its products. Despite numerous efforts to combat biofilm formation, there is still no effective technological means to thoroughly solve the biofilm problem in the dairy industry. Here, we introduced peptide-based coating in order to modify the physical properties of the stainless steel surface by affecting its availability for bacterial adhesion. We found that the coated surface displays a notable decrease in the ability of bacterial cells to attach and to subsequently form biofilm by Gram-positive Bacillus licheniformis and Gram-negative Pseudomonas aeruginosa. Furthermore, the coated surface retained its anti-biofilm ability following its exposure to raw milk. Importantly, the modified surface did not affect the milk coagulation process or its nutritious properties and quality. Overall, this anti-biofilm approach may serve as an attractive solution for the dairy industry in its struggle against bacterial contamination.

Expanding the Functional Scope of the Fmoc-Diphenylalanine Hydrogelator by Introducing a Rigidifying and Chemically Active Urea Backbone Modification.

Peptidomimetic low-molecular-weight hydrogelators, a class of peptide-like molecules with various backbone amide modifications, typically give rise to hydrogels of diverse properties and increased stability compared to peptide hydrogelators. Here, a new peptidomimetic low-molecular-weight hydrogelator is designed based on the well-studied N-fluorenylmethoxycarbonyl diphenylalanine (Fmoc-FF) peptide by replacing the amide bond with a frequently employed amide bond surrogate, the urea moiety, aiming to increase hydrogen bonding capabilities. This designed ureidopeptide, termed Fmoc-Phe-NHCONH-Phe-OH (Fmoc-FuF), forms hydrogels with improved mechanical properties, as compared to those formed by the unmodified Fmoc-FF. A combination of experimental and computational structural methods shows that hydrogen bonding and aromatic interactions facilitate Fmoc-FuF gel formation. The Fmoc-FuF hydrogel possesses properties favorable for biomedical applications, including shear thinning, self-healing, and in vitro cellular biocompatibility. Additionally, the Fmoc-FuF, but not Fmoc-FF, hydrogel presents a range of functionalities useful for other applications, including antifouling, slow release of urea encapsulated in the gel at a high concentration, selective mechanical response to fluoride anions, and reduction of metal ions into catalytic nanoparticles. This study demonstrates how a simple backbone modification can enhance the mechanical properties and functional scope of a peptide hydrogel.

Tailoring the self-assembly of a tripeptide for the formation of antimicrobial surfaces.

The accumulation of bacteria on surfaces is currently one of the greatest concerns for the management of proper healthcare systems, water and energy. Here, we describe the mechanism by which a single peptide forms two pH-dependent supramolecular particles that resist bacterial contamination. By using NMR and molecular dynamics (MD), we determined the structures of the peptide monomers and showed the forces directing the self-assembly of each structure under different conditions. These peptide assemblies change the characteristics of bare glass and confer it with the ability to prevent biofilm formation. Furthermore, they can adsorb and release active compounds as demonstrated with an anticancer drug, antibiotic and enzyme. This synergism and the detailed understanding of the processes are necessary for developing new sterile surfaces for healthcare systems, water purification devices, food packaging or any environment that suffers from biocontamination.

Rational Design of Amphiphilic Peptides and Its Effect on Antifouling Performance.

Biofouling, the unwanted adhesion of organisms to surfaces, has a negative impact on energy, food, water, and health resources. One possible strategy to fight biofouling is to modify the surface using a peptide-based coating that will change the surface properties. We reveal the importance of rational design and positioning of individual amino acids in an amphiphilic peptide sequence. By just manipulating the position of the amino acids within the peptide chain having the same chemical composition, we improved the antifouling performance of an amphiphilic peptide-based coating, Phe(4-F)-Lys-DOPA, by 30%. We have judiciously tailored the peptide configurations to achieve the best antifouling performance by (i) positioning the amino acid lysine adjacent to the DOPA moiety in the linear peptide chain for better adhesion, (ii) having a linear fluorinated N-terminal to improve the packing density of the film by straightening the peptide chain, and (iii) placing DOPA at the C-terminal. We have also compared the antifouling performances of amphiphilic, hydrophobic, hydrophilic, and alternately arranged peptides. Our results show a reduction of ∼80% in bacterial adhesion for an amphiphilic peptide-coated surface when compared to a bare titanium surface. This work provides important strategic design guidelines for future peptide-related materials that have effective antifouling properties.

Electrochemical Approach for Effective Antifouling and Antimicrobial Surfaces.

Biofouling, the adsorption of organisms to a surface, is a major problem today in many areas of our lives. This includes: (i) health, as biofouling on medical device leads to hospital-acquired infections, (ii) water, since the accumulation of organisms on membranes and pipes in desalination systems harms the function of the system, and (iii) energy, due to the heavy load of the organic layer that accumulates on marine vessels and causes a larger consumption of fuel. This paper presents an effective electrochemical approach for generating antifouling and antimicrobial surfaces. Distinct from previously reported antifouling or antimicrobial electrochemical studies, we demonstrate the formation of a hydrogen gas bubble layer through the application of a low-voltage square-waveform pulses to the conductive surface. This electrochemically generated gas bubble layer serves as a separation barrier between the surroundings and the target surface where the adhesion of bacteria can be deterred. Our results indicate that this barrier could effectively reduce the adsorption of bacteria to the surface by 99.5%. We propose that the antimicrobial mechanism correlates with the fundamental of hydrogen evolution reaction (HER). HER leads to an arid environment that does not allow the existence of live bacteria. In addition, we show that this drought condition kills the preadhered bacteria on the surface due to water stress. This work serves as the basis for the exploration of future self-sustainable antifouling techniques such as incorporating it with photocatalytic and photoelectrochemical reactions.

Bio-inspired antifouling approaches: the quest towards non-toxic and non-biocidal materials.

Biofouling is an undesirable process in which organisms and their by-products encrust a surface. Antifouling solutions are of great importance since biofouling has negative effects on numerous species, ecosystems, and areas including water treatment facilities, health-care systems, and marine devices. Many useful solutions have been developed in the last few decades. However, with the emergence of environmental issues, the search for new promising non-toxic materials has expanded. One approach tries to mimic natural antifouling surfaces and relies on mechanisms of action derived from nature. Since these materials are based on natural systems, they are mostly biocompatible and more efficient against complex fouling. In this review, we cover the latest advances in the field of antifouling materials. We specifically focus on biomaterials that are based on the chemical and physical behavior of biological systems.

Self-assembly of a tripeptide into a functional coating that resists fouling.

This communication describes the self-assembly of a tripeptide into a functional coating that resists biofouling. Using this peptide-based coating we were able to prevent protein adsorption and interrupt biofilm formation. This coating can be applied on numerous substrates and therefore can serve in applications related to health care, marine and water treatment.

Co-assembly of aromatic dipeptides into spherical structures that are similar in morphology to red and white blood cells.

This paper describes the co-assembly of two aromatic dipeptides, diphenylalanine and Fmoc-l-DOPA(acetonated)-d-Phe-OMe, into different spherical structures that are similar in morphology to either red or white blood cells. Under the examined experimental conditions, each of the peptides formed spherical nanostructures, but a mixture of the two peptides generated new types of assemblies. When the concentration of the two peptides was 1 mg mL-1 they self-assembled into oval biconcave disk nanostructures that are similar in morphology to red blood cells. When the concentration of the peptides was higher they formed spherical structures with bulges on their outer surface. These assemblies are similar in morphology to white blood cells. We determined the morphology and structure of the assemblies using atomic force microscopy and electron microscopy and their secondary structure using ATR-FTIR and CD. In addition, we studied the co-assembly of Fmoc-DOPA(acetonated)-d-Phe-OMe with other diphenylalanine analogues. Furthermore, we showed that the red blood cell-like structures can adsorb and release the anticancer drug, doxorubicin, and therefore might be useful as a system for sustained drug release.