Specific Cationic Antimicrobial Peptides Enhance the Recovery of Low-Load Quiescent Mycobacterium tuberculosis in Routine Diagnostics.

The culture confirmation of Mycobacterium tuberculosis (MTB) remains the gold standard for the diagnosis of Tuberculosis (TB) with culture conversion representing proof of cure. However, over 40% of TB samples fail to isolate MTB even though many patients remain infectious due to the presence of viable non-culturable forms. Previously, we have shown that two short cationic peptides, T14D and TB08L, induce a hormetic response at low concentrations, leading to a stimulation of growth in MTB and the related animal pathogen Mycobacterium bovis (bTB). Here, we examine these peptides showing they can influence the mycobacterial membrane integrity and function through membrane potential reduction. We also show this disruption is associated with an abnormal reduction in transcriptomic signalling from specific mycobacterial membrane sensors that normally monitor the immediate cellular environment and maintain the non-growing phenotype. We observe that exposing MTB or bTB to these peptides at optimal concentrations rapidly represses signalling mechanisms maintaining dormancy phenotypes, which leads to the promotion of aerobic metabolism and conversion into a replicative phenotype. We further show a practical application of these peptides as reagents able to enhance conventional routine culture methods by stimulating mycobacterial growth. We evaluated the ability of a peptide-supplemented sample preparation and culture protocol to isolate the MTB against a gold standard routine method tested in parallel on 255 samples from 155 patients with suspected TB. The peptide enhancement increased the sample positivity rate by 46% and decreased the average time to sample positivity of respiratory/faecal sampling by seven days. The most significant improvements in isolation rates were from sputum smear-negative low-load samples and faeces. The peptide enhancement increased sampling test sensitivity by 19%, recovery in samples from patients with a previously culture-confirmed TB by 20%, and those empirically treated for TB by 21%. We conclude that sample decontamination and culture enhancement with D-enantiomer peptides offer good potential for the much-needed improvement of the culture confirmation of TB.

Fluorine Substitution of TCNQ Alters the Redox-Driven Catalytic Pathway for the Ferricyanide-Thiosulfate Reaction.

Mechanistic variation in catalysis through substituent-based redox tuning is well established. Fluorination of TCNQ (TCNQ=tetracyanoquinodimethane) provides ~850 mV variation in the redox potentials of the TCNQF n 0 / 1 - ${{{\rm {TCNQF}}}_{{\rm {n}}}^{{\rm {0/1-}}}}$ and TCNQF n 1 - / 2 - ${{{\rm {TCNQF}}}_{{\rm {n}}}^{{\rm {1-/2-}}}}$ (n=0, 2, 4) processes. With TCNQF 4 1 - ${{{\rm {TCNQF}}}_{{\rm {4}}}^{{\rm {1-}}}}$ , catalysis of the kinetically very slow ferrocyanide-thiosulfate redox reaction in aqueous solution occurs via a mechanism in which the catalyst TCNQF 4 1 - ${{{\rm {TCNQF}}}_{{\rm {4}}}^{{\rm {1-}}}}$ is reduced to TCNQF 4 2 - ${{{\rm {TCNQF}}}_{{\rm {4}}}^{{\rm {2-}}}}$ when reacting with S 2 O 3 2 - ${{{\rm {S}}}_{{\rm {2}}}{{\rm {O}}}_{{\rm {3}}}^{{\rm {2-}}}}$ which is oxidised to S 4 O 6 2 - ${{{\rm {S}}}_{{\rm {4}}}{{\rm {O}}}_{{\rm {6}}}^{{\rm {2-}}}}$ . Subsequently, TCNQF 4 2 - ${{{\rm {TCNQF}}}_{{\rm {4}}}^{{\rm {2-}}}}$ reacts with [ Fe ( CN ) 6 ]​ 3 - ${{{\rm {[Fe(CN)}}}_{{\rm {6}}}{{\rm {]}}}^{{\rm {3-}}}}$ to form [ Fe ( CN ) 6 ]​ 4 - ${{{\rm {[Fe(CN)}}}_{{\rm {6}}}{{\rm {]}}}^{{\rm {4-}}}}$ and reform the TCNQF 4 1 - ${{{\rm {TCNQF}}}_{{\rm {4}}}^{{\rm {1-}}}}$ catalyst, in another thermodynamically favoured process. An analogous mechanism applies with TCNQF 2 1 - ${{{\rm {TCNQF}}}_{{\rm {2}}}^{{\rm {1-}}}}$ as a catalyst. In contrast, since the reaction of S 2 O 3 2 - ${{{\rm {S}}}_{{\rm {2}}}{{\rm {O}}}_{{\rm {3}}}^{{\rm {2-}}}}$ with TCNQ 1 - ${{{\rm {TCNQ}}}^{{\rm {1-}}}}$ is thermodynamically unfavourable, an alternative mechanism is required to explain the catalytic activity observed in this non-fluorinated system. Here, upon addition of TCNQ 1 - ${{{\rm {TCNQ}}}^{{\rm {1-}}}}$ , reduction of [ Fe ( CN ) 6 ]​ 3 - ${{{\rm {[Fe(CN)}}}_{{\rm {6}}}{{\rm {]}}}^{{\rm {3-}}}}$ to [ Fe ( CN ) 6 ]​ 4 - ${{{\rm {[Fe(CN)}}}_{{\rm {6}}}{{\rm {]}}}^{{\rm {4-}}}}$ occurs with concomitant oxidation of TCNQ 1 - ${{{\rm {TCNQ}}}^{{\rm {1-}}}}$ to TCNQ 0 ${{{\rm {TCNQ}}}^{{\rm {0}}}}$ , which then acts as the catalyst for S 2 O 3 2 - ${{{\rm {S}}}_{{\rm {2}}}{{\rm {O}}}_{{\rm {3}}}^{{\rm {2-}}}}$ oxidation. Thermodynamic data explain the observed differences in the catalytic mechanisms. CuTCNQF n ${{{\rm {CuTCNQF}}}_{{\rm {n}}}}$ (n=0, 4) also act as catalysts for the ferricyanide-thiosulfate reaction in aqueous solution. The present study shows that homogeneous pathways are available following addition of these dissolved materials. Previously, these CuTCNQF n ${{{\rm {CuTCNQF}}}_{{\rm {n}}}}$ (n=0, 4) coordination polymers have been regarded as insoluble in water and proposed as heterogeneous catalysts for the ferricyanide-thiosulfate reaction. Details and mechanistic differences were established using UV-visible spectrophotometry and cyclic voltammetry.

Membrane interaction and selectivity of novel alternating cationic lipid-nanodisc assembling polymers.

Synthetic polymer nanodiscs are self-assembled structures formed from amphipathic copolymers encapsulating membrane proteins and surrounding phospholipids into water soluble discs. These nanostructures have served as an analytical tool for the detergent free solubilisation and structural study of membrane proteins (MPs) in their native lipid environment. We established the polymer-lipid nanodisc forming ability of a novel class of amphipathic copolymer comprised of an alternating sequence of N-alkyl functionalised maleimide (AlkylM) of systematically varied hydrocarbon chain length, and cationic N-methyl-4-vinyl pyridinium iodide (MVP). Using a combination of physicochemical techniques, the solubilisation efficiency, size, structure and shape of DMPC lipid containing poly(MVP-co-AlkylM) nanodiscs were determined. Lipid solubilisation increased with AlkylM hydrocarbon chain length from methyl (MM), ethyl (EtM), n-propyl (PM), iso-butyl (IBM) through to n-butyl (BM) maleimide bearing polymers. More hydrophobic derivatives formed smaller sized nanodiscs and lipid ordering within poly(MVP-co-AlkylM) nanodiscs was affected by nanodisc size. In dye-release assays, shorter N-alkyl substituted polymers, particularly poly(MVP-co-EtM), exhibited low activities against eukaryotic mimetic POPC membrane and increased their liposome disruption as POPC : POPG membrane mixtures increased in their anionic POPG component, resembling the charge profile of bacterial membranes. These trends in membrane selectivity were transferred towards native cell systems in which gram-positive Staphylococcus aureus and gram-negative Acenobacter baumannii bacterial strains were relatively susceptible to disruption by hydrophobic n-butyl- and n-propyl-poly(MVP-co-AlkylM) derivatives compared to human red blood cells (HRBCs), with a more pronounced selectivity resulting from poly(MVP-co-PM). Such selective membrane interaction by less hydrophobic polymers provides a framework for polymer design towards applications including selective membrane component solubilisation, biosensing and antimicrobial development.

Revisiting the TCNQF 4 0 / 1 - / 2 - ${{\bf TCNQF}_{\bf 4}

The front cover artwork was done by Michelle Farrelly, a member of the Martin group at Monash University. The image represents a perspective of a cuvette in which the catalysis of the thiosulfate-ferricyanide reaction was achieved by a TCNQF4 -based redox reaction in aqueous solution. The primary method used to monitor these reactions was spectrophotometry. Read the full text of the Research Article at 10.1002/cphc.202200942.

Comparative yields of antimicrobial peptides released from human and cow milk proteins under infant digestion conditions predicted by in silico methodology.

Mammalian milk proteins are known to encrypt antimicrobial peptides (AMPs) which can be passively released and exert bioactivity in the gastrointestinal and cardiovascular systems pre- or post-absorption, respectively. However, the contribution of 'passive' food-derived AMPs to the pool of endogenous and microbial AMPs has not been differentiated in previous research. Insight into the consequences of protein digestion and peptide bioactivity can be gained using in silico tools. The aim of this investigation was to use in silico methods to characterise the yields of AMPs released from major proteins in human and cow milk under infant digestion conditions, as relevant to early nutrition. The profiles of major proteins in human and cow milk from UniProtKB/Swiss-Prot, were subjected to in silico digestion by ExPASy-PeptideCutter, and the AMP activity of resulting peptides (≥4 amino acids, AAs) evaluated with the CAMPR3-RF predictive tool. The mass yields and counts of absorbing (≤10 AAs) and non-absorbing (>10 AAs) AMPs, as found in human, cow and 'humanised' ratios of cow milk proteins, were quantified. The results indicated that major whey proteins from both human and cow milks displayed a higher degree of hydrolysis than caseins, consistent with their known 'fast' digestion properties. Larger albumin and lactoferrin proteins generated relatively more and/or longer peptides. Yields of AMPs from cow milk were higher than from human milk, even after standardising the ratio of whey to casein and total protein concentration, as practiced in formulations manufactured for human newborn babies. Whereas alpha-lactalbumin (2.65 g L-1) and lactoferrin (1.75 g L-1) provided the major yields of AMPs in human milk whey proteins; beta-lactoglobulin, which is unique to cow milk, released the highest yield of AMPs in cow milk (3.25 g L-1 or 19.9% w/w of total whey protein), which may represent an important and overlooked biological function of this protein in cow milk.

Lipid oxidation controls peptide self-assembly near membranes through a surface attraction mechanism.

The self-assembly of peptides into supramolecular structures has been linked to neurodegenerative diseases but has also been observed in functional roles. Peptides are physiologically exposed to crowded environments of biomacromolecules, and particularly cellular membrane lipids. Previous research has shown that membranes can both accelerate and inhibit peptide self-assembly. Here, we studied the impact of membrane models that mimic cellular oxidative stress and compared this to mammalian and bacterial membranes. Using molecular dynamics simulations and experiments, we propose a model that explains how changes in peptide-membrane binding, electrostatics, and peptide secondary structure stabilization determine the nature of peptide self-assembly. We explored the influence of zwitterionic (POPC), anionic (POPG) and oxidized (PazePC) phospholipids, as well as cholesterol, and mixtures thereof, on the self-assembly kinetics of the amyloid ß (1-40) peptide (Aß40), linked to Alzheimer's disease, and the amyloid-forming antimicrobial peptide uperin 3.5 (U3.5). We show that the presence of an oxidized lipid had similar effects on peptide self-assembly as the bacterial mimetic membrane. While Aß40 fibril formation was accelerated, U3.5 aggregation was inhibited by the same lipids at the same peptide-to-lipid ratio. We attribute these findings and peptide-specific effects to differences in peptide-membrane adsorption with U3.5 being more strongly bound to the membrane surface and stabilized in an α-helical conformation compared to Aß40. Different peptide-to-lipid ratios resulted in different effects. We found that electrostatic interactions are a primary driving force for peptide-membrane interaction, enabling us to propose a model for predicting how cellular changes might impact peptide self-assembly in vivo.

Revisiting the TCNQF4 0/1-/2- Catalysis Mechanism for the [Fe(CN)6 ]3-/4- -S2 O3 2- /S4 O6 2- Redox Reaction.

Published data suggest that sparingly soluble metal complexes of TCNQF n 1 - ${{\rm{TCNQF}}_{\rm{n}}^{{\rm{1 - }}} }$ , where n=0, 1, 2, 4, can act as heterogeneous catalysts for the kinetically very slow [ Fe ( CN ) 6 ]​ 3 - / 4 - ${{\rm{[Fe(CN)}}_{\rm{6}} {\rm{]}}^{{\rm{3 - /4 - }}} }$ - S 2 O 3 2 - ${{\rm{S}}_{\rm{2}} {\rm{O}}_{\rm{3}}^{{\rm{2 - }}} }$ / S 4 O 6 2 - ${{\rm{S}}_{\rm{4}} {\rm{O}}_{\rm{6}}^{{\rm{2 - }}} }$ reaction in aqueous solution. This study shows that the coordination polymer CuTCNQF 4 ${{\rm{CuTCNQF}}_{\rm{4}} }$ , participates as a homogeneous catalyst via an extremely small concentration of dissolved TCNQF 4 1 - ${{\rm{TCNQF}}_{\rm{4}}^{{\rm{1 - }}} }$ . This finding suggests that the generally accepted mechanism of catalysis by TCNQF 4 ${{\rm{TCNQF}}_{\rm{4}} }$ based solids needs to be revisited to ascertain the role of homogeneous pathways. In the present study, UV-visible spectrophotometry was used to examine the catalysis of the aqueous redox reaction of [ Fe ( CN ) 6 ]​ 3 - ${{\rm{[Fe(CN)}}_{\rm{6}} {\rm{]}}^{{\rm{3 - }}} }$ (1.0 mM) with S 2 O 3 2 - ${{\rm{S}}_{\rm{2}} {\rm{O}}_{\rm{3}}^{{\rm{2 - }}} }$ (100 mM) in the presence of (i) a precursor catalyst, TCNQF 4 0 ${{\rm{TCNQF}}_{\rm{4}}^{\rm{0}} }$ ; (ii) the catalyst, TCNQF 4 1 - ${{\rm{TCNQF}}_{\rm{4}}^{{\rm{1 - }}} }$ , as the water soluble Li+ salt; and (iii) CuTCNQF 4 ${{\rm{CuTCNQF}}_{\rm{4}} }$ . A homogeneous reaction scheme that utilises the TCNQF 4 1 - / 2 - ${{\rm{TCNQF}}_{\rm{4}}^{{\rm{1 - /2 - }}} }$ couple is provided. In the case of TCNQF 4 1 - ${{\rm{TCNQF}}_{\rm{4}}^{{\rm{1 - }}} }$ derived from highly soluble LiTCNQF 4 ${{\rm{LiTCNQF}}_{\rm{4}} }$ , quantitative conversion of 1.0 mM S 2 O 3 2 - ${{\rm{S}}_{\rm{2}} {\rm{O}}_{\rm{3}}^{{\rm{2 - }}} }$ to 0.50 mM S 4 O 6 2 - ${{\rm{S}}_{\rm{4}} {\rm{O}}_{\rm{6}}^{{\rm{2 - }}} }$ occurs with complete reduction of [ Fe ( CN ) 6 ]​ 3 - ${{\rm{[Fe(CN)}}_{\rm{6}} {\rm{]}}^{{\rm{3 - }}} }$ to [ Fe ( CN ) 6 ]​ 4 - ${{\rm{[Fe(CN)}}_{\rm{6}} {\rm{]}}^{{\rm{4 - }}} }$ being rapidly accelerated by sub-micomolar concentrations of TCNQF 4 1 - ${{\rm{TCNQF}}_{\rm{4}}^{{\rm{1 - }}} }$ . TCNQF 4 2 - ${{\rm{TCNQF}}_{\rm{4}}^{{\rm{2 - }}} }$ generated in the catalytic cycle, reacts with [ Fe ( CN ) 6 ]​ 3 - ${{\rm{[Fe(CN)}}_{\rm{6}} {\rm{]}}^{{\rm{3 - }}} }$ to reform TCNQF 4 1 - ${{\rm{TCNQF}}_{\rm{4}}^{{\rm{1 - }}} }$ and produce [ Fe ( CN ) 6 ]​ 4 - ${{\rm{[Fe(CN)}}_{\rm{6}} {\rm{]}}^{{\rm{4 - }}} }$ . Along with the rapid catalytic reaction, the sluggish competing reaction between TCNQF 4 1 - ${{\rm{TCNQF}}_{\rm{4}}^{{\rm{1 - }}} }$ and S 2 O 3 2 - ${{\rm{S}}_{\rm{2}} {\rm{O}}_{\rm{3}}^{{\rm{2 - }}} }$ occurs to give TCNQF 4 2 - ${{\rm{TCNQF}}_{\rm{4}}^{{\rm{2 - }}} }$ , which is protonated to HTCNQF 4 1 - ${{\rm{\;HTCNQF}}_{\rm{4}}^{{\rm{1 - }}} }$ , along with a trace amount of S 4 O 6 2 - ${{\rm{S}}_{\rm{4}} {\rm{O}}_{\rm{6}}^{{\rm{2 - }}} }$ . On addition of the precursor catalyst, TCNQF 4 0 ${{\rm{TCNQF}}_{\rm{4}}^{\rm{0}} }$ , rapid reduction with S 2 O 3 2 - ${{\rm{S}}_{\rm{2}} {\rm{O}}_{\rm{3}}^{{\rm{2 - }}} }$ occurs to form TCNQF 4 1 - ${{\rm{TCNQF}}_{\rm{4}}^{{\rm{1 - }}} }$ - the active catalyst. CuTCNQF 4 ${{\rm{CuTCNQF}}_{\rm{4}} }$ added to water is shown to be sufficiently soluble to provide adequate TCNQF 4 1 - ${{\rm{TCNQF}}_{\rm{4}}^{{\rm{1 - }}} }$ to act as the catalyst for the [ Fe ( CN ) 6 ]​ 3 - / 4 - ${{\rm{[Fe(CN)}}_{\rm{6}} {\rm{]}}^{{\rm{3 - /4 - }}} }$ - S 2 O 3 2 - ${{\rm{S}}_{\rm{2}} {\rm{O}}_{\rm{3}}^{{\rm{2 - }}} }$ / S 4 O 6 2 - ${{\rm{S}}_{\rm{4}} {\rm{O}}_{\rm{6}}^{{\rm{2 - }}} }$ reaction.

Helical intermediate formation and its role in amyloids of an amphibian antimicrobial peptide.

Helical intermediates appear to be crucial in the amyloid formation of several amyloidogenic peptides, including Aß, that are implicated in different neurodegenerative diseases. Intermediate species of amyloid formation have been reported to be more toxic than mature amyloid fibrils. Hence, the current work focuses on understanding the mechanistic roles of the helical intermediates in the early stages of amyloid self-assembly in amyloidogenic peptides. Molecular dynamics (MD) simulations and the adaptive biasing force (ABF) method were utilized to investigate structural changes that lead to amyloid formation in amphibian peptide uperin-3.5 (U3.5), an antimicrobial and amyloidogenic peptide. Microsecond time-scale MD simulations revealed that peptide aggregation, into ß-sheet dominated aggregates, is centred on two important factors; evolution of α-helical intermediates and the critical role of local peptide concentration inside these aggregates. Electrostatic attraction between the oppositely charged aspartate (D) and arginine (R) residues located near the N-terminus induced hydrogen bonding resulting in the formation of precursor 310-helices close to the N-terminus. The 310-helices transitioned into α-helices, thereby imparting partial helical conformations to the peptides. In the initial stages of aggregation, U3.5 peptides with amphipathic, partial helices were driven closer by hydrophobic interactions to form small clusters of helical intermediates. These helices imparted stability to the helical intermediates, which promoted the growth of clusters by further addition of peptides. This led to an increase in the local peptide concentration, which enabled stronger peptide-peptide interactions and triggered a ß-sheet transition in these aggregates. Thus, this study emphasized that the helical intermediates may be crucial to the evolution of ß-sheet-rich amyloid structures.

Peptide Self-Assembly into Amyloid Fibrils at Hard and Soft Interfaces-From Corona Formation to Membrane Activity.

Peptides and proteins are exposed to a variety of interfaces in a physiological environment, such as cell membranes, protein nanoparticles (NPs), or viruses. These interfaces have a significant impact on the interaction, self-assembly, and aggregation mechanisms of biomolecular systems. Peptide self-assembly, particularly amyloid fibril formation, is associated with a wide range of functions; however, there is a link with neurodegenerative diseases, such as Alzheimer's disease. This review highlights how interfaces affect peptide structure and the kinetics of aggregation leading to fibril formation. In nature, many surfaces are nanostructures, such as liposomes, viruses, or synthetic NPs. Once exposed to a biological medium, nanostructures are coated with a corona, which then determines their activity. Both accelerating and inhibiting effects on peptide self-assembly have been observed. When amyloid peptides adsorb to a surface, they typically concentrate locally, which promotes aggregation into insoluble fibrils. Starting from a combined experimental and theoretical approach, models that allow for a better understanding of peptide self-assembly near hard and soft matter interfaces are introduced and reviewed. Research results from recent years are presented and relationships between biological interfaces, such as membranes and viruses, and amyloid fibril formation are proposed.

Live bio-nano-sonosensitizer targets malignant tumors in synergistic therapy.

Sonosensitizers that can increase the concentration of reactive oxygen species (ROS) within a tumor microenvironment is a high priority for sonodynamic therapy (SDT). In this study, a functionalized, smart nanosonosensitizer based on Au-RuO2 nanoparticles (NPs) and selenium nanoparticles (Se NPs) that were electrostatically self-assembled onto the surface of Listeria innocua (LI) was used to create Bac@ARS. Au NPs provided the core in which RuO2 was deposited to form Au-RuO2 NPs. Additionally, the underlying properties of the Au NPs and Se NPs were used to optimize the sonosensitivity performance. Compared with pristine RuO2 NPs, Bac@ARS exhibits highly efficient ROS-producing activity. Furthermore, Bac@ARS remodeled the hypoxic tumor microenvironment, enabling overproduction of ROS. Importantly, Bac@ARS exploits the natural tropism of LI to selectively accumulate in tumors, which improved the treatment precision at hypoxic tumor sites after sonodynamic activation. However, the activity of LI was greatly reduced after ultrasound (US) irradiation, ensuring the biosafety of Bac@ARS. Bac@ARS was also used to monitor tumors, in real time, using photoacoustic imaging of the gold-based nanoparticles. Therefore, Bac@ARS is a promising microbial sonosensitizer providing a new platform for the optimization of sonosensitizers for tumor treatment. STATEMENT OF SIGNIFICANCE: A bio-nano-sonosensitizer was designed using a Au nanoparticle (NP) core modified with RuO2 NPs. The Au-RuO2 NPs together with Se-NPs are attached via electrostatic adsorption to a live bacterium Listeria innocua (LI), creating Bac@ARS. The role of the NPs was to optimize the sonosensitivity performance at the target tumor site. Bac@ARS reshaped the tumor microenvironment and overcame tumor hypoxia leading to ROS overproduction. This activated a potent ICD-mediated cellular immunity and anti-tumor activity. Importantly, Bac@ARS exploited the natural tropism of LI to selectively accumulate in tumors, resulting in more precise delivery of the therapeutic effect while exhibiting reduced effects on healthy tissues.

Curvature model for nanoparticle size effects on peptide fibril stability and molecular dynamics simulation data.

Nanostructured surfaces are widespread in nature and are being further developed in materials science. This makes them highly relevant for biomolecules, such as peptides. In this data article, we present a curvature model and molecular dynamics (MD) simulation data on the influence of nanoparticle size on the stability of amyloid peptide fibrils related to our research article entitled "Mechanistic insights into the size-dependent effects of nanoparticles on inhibiting and accelerating amyloid fibril formation" (John et al., 2022) [1]. We provide the code to perform MD simulations in GROMACS 4.5.7 software of arbitrarily chosen biomolecule oligomers adsorbed on a curved surface of chosen nanoparticle size. We also provide the simulation parameters and data for peptide oligomers of Aß40, NNFGAIL, GNNQQNY, and VQIYVK. The data provided allows researchers to further analyze our MD simulations and the curvature model allows for a better understanding of oligomeric structures on surfaces.

Self-Assembly of Linear, Natural Antimicrobial Peptides: An Evolutionary Perspective.

Antimicrobial peptides are an ancient and innate system of host defence against a wide range of microbial assailants. Mechanistically, unstructured peptides undergo a secondary structure transition into amphipathic α-helices, upon contact with membrane surfaces. This leads to peptide binding and removal of the membrane components in a detergent-like manner or via self-organisation into trans-membrane pores (either barrel-stave or toroidal pore) thereby destroying the microbe. Self-assembly of antimicrobial peptides into oligomers and ultimately amyloid has been mostly examined in parallel, however recent findings link diseases, such as Alzheimer's disease as an aberrant activity of a protective neuropeptide with antimicrobial activity. These self-assembled oligomers can also interact with membranes. Here, we review those antimicrobial peptides reported to self-assemble into amyloid, where supported by structural evidence. We consider their membrane activities as antimicrobial peptides and present evidence of consistent self-assembly patterns across major evolutionary groups. Trends are apparent across these groups, supporting the mounting data that self-assembly of antimicrobial peptides into amyloid should be considered as synergistic to the antimicrobial peptide response.

Mechanistic insights into the size-dependent effects of nanoparticles on inhibiting and accelerating amyloid fibril formation.

The aggregation of peptides into amyloid fibrils has been linked to ageing-related diseases, such as Alzheimer's and type 2 diabetes. Interfaces, particularly those with large nanostructured surfaces, can affect the kinetics of peptide aggregation, which ranges from complete inhibition to strong acceleration. While a number of physiochemical parameters determine interfacial effects, we focus here on the role of nanoparticle (NP) size and curvature. We used thioflavin T (ThT) fluorescence assays to demonstrate the size-dependent effects of NPs on amyloid fibril formation for the peptides Aß40, NNFGAIL, GNNQQNY and VQIYVK. While 5 nm gold NPs (AuNP-5) retarded or inhibited the aggregation of all peptides except NNFGAIL, larger 20 nm gold NPs (AuNP-20) tended to accelerate or not influence peptide aggregation. Differences in the NP effects for the peptides resulted from the different peptide properties (size, tendency to aggregate) and associated surface binding affinities. Additional dynamic light scattering (DLS), electron microscopy, and atomic force microscopy (AFM) experiments with the Aß40 peptide confirmed size-dependent NP effects on peptide aggregation, and also suggested a structural influence on the formed fibrils. NPs can serve as a surface for the adsorption of peptide monomers and enable nucleation to oligomers and fibril formation. However, molecular dynamics (MD) simulations showed that peptide oligomers were less stable at smaller NPs. High surface curvatures destabilized prefibrillar structures, which provides a possible explanation for inhibitory effects on fibril growth, provided that peptide-NP surface binding was relevant for fibril formation. These mechanistic insights can support the design of future nanostructured materials.

Secondary Structure Transitions for a Family of Amyloidogenic, Antimicrobial Uperin 3 Peptides in Contact with Sodium Dodecyl Sulfate.

Secondary structure changes are an inherent part of antimicrobial (AMP) and amyloidogenic peptide activity, especially in close proximity to membranes, and impact the peptides' function and dysfunction roles. The formation, and stability of α-helical components are regarded as essential 'intermediates' for both these functions. To illuminate the conformational transitions leading to amyloid formation we use short cationic AMPs, from an Australian toadlet, Uperoleia mjobergii, (Uperin 3 family, U3) and assess the impact on secondary structural elements in the presence of a membrane mimetic surfactant, sodium dodecyl sulfate (SDS). Specifically, Uperin 3.x, where x=4, 5, 6 wild-type peptides and position seven variants for each, R7A or K7A, were investigated using a combination of experimental and simulation approaches. In water, U3 peptides remain largely unstructured as random coils, with the addition of salts initiating structural transitions leading to assembly towards amyloid. Solution NMR data show that an unstructured U3.5 wt peptide transitions in the presence of SDS to a well-defined α-helical structure that spans nearly the entire sequence. Circular dichroism (CD) and ThT fluorescence studies show that all six U3 peptides aggregate in solution, albeit with vastly varying rates, and a dynamic equilibrium between soluble aggregates rich in either α-helices or ß-sheets may exist in solution. However, the addition of SDS leads to a rapid disaggregation for all peptides and stabilisation of predominantly α-helical content in all the U3 peptides. Molecular dynamics (MD) simulations show that the adsorption of U3.5 wt/R7A peptides onto the SDS micelle is driven by Coulombic attraction between peptide cationic residues and the negatively charged sulfate head-groups on SDS. Simulating the interactions of various kinds of ß-sheet dimers (of both U3.5 wt and its variant U3.5 R7A) with SDS micelles confirmed ß-sheet content decreases in the dimers after their attachment to the SDS micelle. Adsorbed peptides interact favourably with the hydrophobic core of the micelle, promoting intramolecular hydrogen bonds leading to stabilisation of the α-helical structure in peptides, and resulting in a corresponding decrease in intermolecular hydrogen bonds responsible for ß-sheets.

Polymer Nanodiscs and Their Bioanalytical Potential.

Membrane proteins (MPs) play a pivotal role in cellular function and are therefore predominant pharmaceutical targets. Although detailed understanding of MP structure and mechanistic activity is invaluable for rational drug design, challenges are associated with the purification and study of MPs. This review delves into the historical developments that became the prelude to currently available membrane mimetic technologies before shining a spotlight on polymer nanodiscs. These are soluble nanosized particles capable of encompassing MPs embedded in a phospholipid ring. The expanding range of reported amphipathic polymer nanodisc materials is presented and discussed in terms of their tolerance to different solution conditions and their nanodisc properties. Finally, the analytical scope of polymer nanodiscs is considered in both the demonstration of basic nanodisc parameters as well as in the elucidation of structures, lipid-protein interactions, and the functional mechanisms of reconstituted membrane proteins. The final emphasis is given to the unique benefits and applications demonstrated for native nanodiscs accessed through a detergent free process.

Crystalline ruthenium polypyridine nanoparticles: a targeted treatment of bacterial infection with multifunctional antibacterial, adhesion and surface-anchoring photosensitizer properties.

Photodynamic antibacterial therapy employs nanocomposites as an alternative to traditional antibiotics for the treatment of bacterial infections. However, many of these antibacterial materials are less effective towards bacteria than traditional drugs, either due to poor specificity or antibacterial activity. This can result in needless and excessive drug use in treatments. This paper describes a multifunctional drug delivery nanoparticle (MDD-NP), Sph-Ru-MMT@PZ, based on the nanostructured-form of [Ru(bpy)2dppz] (PF6)2 (Sph-Ru), which has adhesive properties towards its microbial targets as well as surface-anchoring photosensitizer effects. The design and construction of MDD-NP is based on the adhesive properties of the outer layers of montmorillonite (MMT), which allows Sph-Ru-MMT@PZ to successfully reach its bacterial target; the outer layer of the E. coli. In addition, under 670 nm red irradiation therapy (R-IT), the surface-anchoring properties use the photosensitizer phthalocyanine zinc (PZ) to destroy the bacteria by producing reactive oxygen species (ROS) which causes cell lysis of E. coli. More importantly, Sph-Ru-MMT@PZ has no fluorescence response to live E. coli with intact cell membranes but selectively stained and demonstrated fluorescence during membrane damage of early-stage cells as well as exposure of nuclear materials at late-stage of cell lysis. Sph-Ru-MMT@PZ showed beneficial and synergistic anti-infective effects in vivo by inhibiting the E. coli infection-induced inflammatory response and eventually promoting wound healing in mice. This new strategy for high precision antibacterial therapy towards specific targets, provides an exciting opportunity for the application of multifunctional nanocomposites towards microbial infections.

Enantiomeric selectivity of ruthenium (II) chiral complexes with antitumor activity, in vitro and in vivo.

Different enantiomers of chiral drugs show distinctive activities. Here, a pair of chiral ruthenium Λ-[Ru(phen)2(TPEPIP)]2+ (Λ-Ru), and Δ-[Ru(phen)2(TPEPIP)]2+ (Δ-Ru) (phen = 1,10-phenanthroline; TPEPIP = 2-(4'-(1,2,2-triphenylvinyl)-[1,1'-biphenyl]-4-yl)-1H-imidazo[4,5-f][1,10]phenanthroline) compounds have been prepared and characterized. Both have aggregation-induced emission characteristics, although Λ-Ru exhibits much higher activity, towards duplex DNA extracted from SGC-7901 cancer cells. In vitro experiments demonstrate that both Λ-Ru and Δ-Ru can induce the apoptosis of tumor cells with Λ-Ru showing greater activity than Δ-Ru. Λ-Ru aggregates in the cell nucleus of SGC-7901 within 5 h which shows that nucleic acids may be the effective target of Λ-Ru. In vivo experiments with nude mice showed that Λ-Ru can inhibit the growth and proliferation of a tumor, in tumor-bearing mice as well as targeting the tumor site, as demonstrated by fluorescence. These results demonstrate the dual-function of Λ-Ru, which could be used for real-time visualization of a chemotherapeutic agent.

Exploring the Role of Peptide Helical Stability in the Propensity of Uperin 3.x Peptides toward Beta-Aggregation.

Antimicrobial peptides of the uperin 3.x family, obtained from the skin secretions of Uperoleia mjobergii, have an inherent ability to form amyloid with possible functional roles and can serve as model peptides to understand mechanistic aspects of amyloidogenesis. The substitution of a positively charged amino acid with a nonpolar alanine residue increased aggregation, fibril content, and propensity for ß-sheet formation for the uperin 3.5 R7A variant when compared with the uperin 3.5 wild-type peptides. We use molecular dynamics (MD) simulations and circular dichroism (CD) measurements on three uperin 3.x peptides and their corresponding seventh position alanine variants to understand the effect of substitution of a positively charged amino acid with a nonpolar alanine residue on the process of ß-aggregation. Both CD experiments and simulations show that the uperin 3.x wild-type peptides demonstrated lower ß-sheet content and propensity than with the corresponding alanine variants. Significantly, simulations of helix-to-coil transitions in individual peptides show an inverse relationship between the helical stability of peptides and their propensity to form structures rich in ß-sheets as observed in CD experiments. A simulation scheme based on a conformational search of helix-to-coil transition trajectories to select peptide conformers was used to assemble propagating peptide oligomers. Whereas octamers consisting of lower helical stability peptide conformers evolve into compact aggregates with a large ß-sheet component, octamers composed of high helical stability conformers disintegrate and show the least amounts of ß-sheet components. The highlight of the current work is that MD simulations are able to predict the correct order of ß-sheet propensity among the six peptides derived from the CD experiments and indicate the importance of helical intermediates in the amyloidogenesis pathway for uperin 3.x peptides.

Sequence comparisons of cytochrome P450 aromatases from Australian animals predict differences in enzymatic activity and/or efficiency†.

Aromatase (P450arom, CYP19A1) is the terminal enzyme in the synthesis of the steroid hormone family of estrogens. Not surprisingly, this enzyme has structural similarities between the limited number of species studied thus far. This study examined the structure of aromatases from four diverse Australian species including a marsupial (tammar wallaby; Macropus eugenii), monotreme (platypus; Ornithorhynchus anatinus), ratite (emu; Dromaius novaehollandiae) and lizard (bearded dragon; Pogona vitticeps). We successfully built homology models for each species, using the only crystallographically determined structure available, human aromatase. The amino acid sequences showed high amino acid sequence identity to the human aromatase: wallaby 81%, platypus 73%, emu 75% and bearded dragon at 74%. The overall structure was highly conserved among the five species, although there were non-secondary structures (loops and bends) that were variable and flexible that may result in some differences in catalytic activity. At the N-terminal regions, there were deletions and variations that suggest that functional distinctions may be found. We found that the active sites of all these proteins were identical, except for a slight variation in the emu. The electrostatic potential across the surfaces of these aromatases highlighted likely variations to the protein-protein interactions of these enzymes with both redox partner cytochrome P450 reductase and possibly homodimerization in the case of the platypus, which has been postulated for the human aromatase enzyme. Given the high natural selection pressures on reproductive strategies, the relatively high degree of conservation of aromatase sequence and structure across species suggests that there is biochemically very little scope for changes to have evolved without the loss of enzyme activity.

Adsorption of Amyloidogenic Peptides to Functionalized Surfaces Is Biased by Charge and Hydrophilicity.

Surfaces are abundant in living systems, such as in the form of cellular membranes, and govern many biological processes. In this study, the adsorption of the amyloidogenic model peptides GNNQQNY, NNFGAIL, and VQIVYK as well as the amyloid-forming antimicrobial peptide uperin 3.5 (U3.5) were studied at low concentrations (100 µM) to different surfaces. The technique of a quartz crystal microbalance with dissipation monitoring (QCM-D) was applied as it enables the monitoring of mass binding to sensors at nanogram sensitivity. Gold-coated quartz sensors were used as unmodified gold surfaces or functionalized with self-assembled monolayers (SAMs) of alkanethiols (terminated as methyl, amino, carboxyl, and hydroxyl) resulting in different adsorption affinities of the peptides. Our objective was to evaluate the underlying role of the nature and feature of interfaces in biological systems which could concentrate peptides and impact or trigger peptide aggregation processes. In overall, the largely hydrophobic peptides adsorbed with preference to hydrophobic or countercharged surfaces. Further, the glycoprotein lubricin (LUB) was tested as an antiadhesive coating. Despite its hydrophilicity, the adsorption of peptides to LUB coated sensors was similar to the adsorption to unmodified gold surfaces, which indicates that some peptides diffused through the LUB layer to reach the underlying gold sensor surface. The LUB protein-antiadhesive is thus more effective as a biomaterial coating against larger biomolecules than small peptides under the conditions used here. This study provides directions toward a better understanding of amyloid peptide adsorption to biologically relevant interfaces, such as cellular membranes.