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Introduction
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March 2013 - January 2021
January 2011 - present
Publications
Publications (235)
Immunoreagents, most commonly antibodies, are integral components of lateral flow immunoassays. However, the use of antibodies comes with limitations, particularly relating to their reproducible production, and poor thermal and chemical stability. Here, we employ phage display to develop affibodies, a class of nonimmunoglobulin affinity proteins ba...
Two‐dimensional (2D) graphene‐based nanomaterials (GNMs) have shown potential in biomedical applications, including diagnostics, therapeutics, and drug delivery, due to their unique combination of properties such as mechanical strength, excellent electrical and thermal conductivity as well as high adsorption capacity which, combined with the ease o...
Staphylococcus aureus is a leading cause of nosocomial implant-associated infections, causing significant morbidity and mortality, underscoring the need for rapid, non-invasive, and cost-effective diagnostics. Here, we optimise the synthesis of renal-clearable gold nanoclusters (AuNCs) for enhanced catalytic activity with the aim of developing a se...
Silica nanoparticles (SNPs), one of the most widely researched materials in modern science, are now commonly exploited in surface coatings, biomedicine, catalysis, and engineering of novel self‐assembling materials. Theoretical approaches are invaluable to enhancing fundamental understanding of SNP properties and behavior. Tremendous research atten...
Human amylin is an inherently disordered protein whose ability to form amyloid fibrils is linked to the onset of type II diabetes. Graphitic nanomaterials have potential in managing amyloid diseases...
Ionic charge transport is a ubiquitous language of communication in biological systems. As such, bioengineering is in constant need of innovative, soft, and biocompatible materials that facilitate ionic conduction. Low molecular weight gelators (LMWGs) are complex self-assembled materials that have received increasing attention in recent years. Bey...
Peptides have great potential as novel biomaterials and therapeutic agents, due to their unique ability to self‐assemble into low dimensional nanostructures, and their resistance to enzymatic degradation in vivo. However, the self‐assembly mechanisms of β‐peptides, which possess increased flexibility due to the extra backbone methylene groups prese...
Due to the variety of roles served by the cell membrane, its composition and structure are complex, making it difficult to study. Bioorthogonal reactions, such as the strain promoted azide‐alkyne cycloaddition (SPAAC), are powerful tools for exploring the function of biomolecules in their native environment but have been largely unexplored within t...
Due to the variety of roles served by the cell membrane, its composition and structure are complex, making it difficult to study. Bioorthogonal reactions, such as the strain promoted azide‐alkyne cycloaddition (SPAAC), are powerful tools for exploring the function of biomolecules in their native environment but have been largely unexplored within t...
It is now evident that the cell manipulates lipid composition to regulate different processes such as membrane protein insertion, assembly and function. Moreover, changes in membrane structure and properties, lipid homeostasis during growth and differentiation with associated changes in cell size and shape, and responses to external stress have bee...
Due to the variety of roles served by the cell membrane, its composition and structure are complex, making it difficult to study. Bioorthogonal reactions, such as the strain promoted azide–alkyne cycloaddition (SPAAC), are powerful tools for exploring the function of biomolecules in their native environment but have been largely unexplored within t...
Peptide self-assembly is the process by which peptide molecules aggregate into low dimensional (1D, 2D) or 3D ordered materials with potential applications ranging from drug delivery to electronics. Short peptides are particularly good candidates for forming supramolecular assemblies due to the relatively simple structure and ease of modulating the...
Flexible metal‐organic materials are of growing interest owing to their ability to undergo reversible structural transformations under external stimuli. Here, we report flexible metal‐phenolic networks (MPNs) featuring stimuli‐responsive behavior to diverse solute guests. The competitive coordination of metal ions to phenolic ligands of multiple co...
Flexible metal–organic materials are of growing interest owing to their ability to undergo reversible structural transformations under external stimuli. Here, we report flexible metal‒phenolic networks (MPNs) featuring stimuli‐responsive behavior to diverse solute guests. The competitive coordination of metal ions to phenolic ligands of multiple co...
Ultrasmall peptide-protected gold nanoclusters are a promising class of bioresponsive material exhibiting pH-sensitive photoluminescence. We present a theoretical insight into the effect peptide-ligand environment has on pH-responsive fluorescence, with the aim of enhancing the rational design of gold nanoclusters for bioapplications. Employing a h...
The ability to predict cell-permeable candidate molecules has great potential to assist drug discovery projects. Large molecules that lie beyond the Rule of Five (bRo5) are increasingly important as drug candidates and tool molecules for chemical biology. However, such large molecules usually do not cross cell membranes and cannot access intracellu...
Coordination states of metal‐organic materials are known to dictate their physicochemical properties and applications in various fields. However, understanding and controlling coordination sites in metal‐organic systems is challenging. Herein, we report the synthesis of site‐selective coordinated metal‐phenolic networks (MPNs) using flavonoids as c...
Polymersomes are vesicular structures self‐assembled from amphiphilic block copolymers and are considered an alternative to liposomes for applications in drug delivery, immunotherapy, biosensing, and as nanoreactors and artificial organelles. However, the limited availability of systematic stability, protein fouling (protein corona formation), and...
Coordination states of metal–organic materials are known to dictate their physicochemical properties and applications in various fields. However, understanding and controlling coordination sites in metal–organic systems is challenging. Herein, we report the synthesis of site‐selective coordinated metal–phenolic networks (MPNs) using flavonoids as c...
Electromagnetic bioeffects remain an enigma from both the experimental and theoretical perspectives despite the ubiquitous presence of related technologies in contemporary life. Multiscale computational modelling can provide valuable insights into biochemical systems and predict how they will be perturbed by external stimuli. At a microscopic level...
Membrane model systems capable of mimicking live cell membranes were used for the first time in studying the effects arising from electromagnetic fields (EMFs) of 18 GHz where membrane permeability was observed following exposure. A present lack of understanding of the mechanisms that drive such a rapid change in membrane permeabilization as well a...
Interfacial modular assembly has emerged as an adaptable strategy for engineering the surface properties of substrates in biomedicine, photonics, and catalysis. Herein, we report a versatile and robust coating (pBDT‐TA), self‐assembled from tannic acid (TA) and a self‐polymerizing aromatic dithiol (i.e., benzene‐1,4‐dithiol, BDT), that can be engin...
Interfacial assemblies are spontaneously formed on various substrates in aqueous conditions via simultaneous covalent and noncovalent interactions using tannic acid and the small aromatic molecule benzene-1,4-dithiol. The robust and colorless coatings enable the subsequent on-surface synthesis or modification for the development of various multifun...
The novel RNA virus, severe acute respiratory syndrome coronavirus II (SARS-CoV-2), is currently the leading cause of mortality in 2020, having led to over 1.6 million deaths and infecting over 75 million people worldwide by December 2020. While vaccination has started and several clinical trials for a number of vaccines are currently underway, the...
The evolution of life on earth eventually leads to the emergence of species with increased complexity and diversity. Similarly, evolutionary chemical space exploration in the laboratory is a key step to pursue the structural and functional diversity of supramolecular systems. Here, we present a powerful tool that enables rapid peptide diversificati...
Non-specific protein adsorption represents a significant challenge for the design of efficient and safe nanoparticles for biomedical applications since it may prevent functional ligands to target the desired specific receptors which can limit the efficacy of novel drug delivery systems and biosensors. The biofilm formation initiated by protein adso...
The orientation-specific immobilization of antibodies onto nanoparticles, to preserve antibody–antigen recognition, is a key challenge in developing targeted nanomedicines. Herein, we report the targeting ability of metal–phenolic network (MPN)-coated gold nanoparticles with surface-physisorbed antibodies against respective antigens. The MPN coatin...
Nonthermal effects of the electromagnetic (EM) field in the radio and microwave frequency ranges on basic biological matter are difficult to detect and thus remain poorly understood. In this work, all-atom nonequilibrium molecular dynamics simulations were performed to investigate the molecular mechanisms of an amyloidogenic peptide response to non...
Label-free surface-enhanced Raman spectroscopy (SERS) can interrogate systems by directly fingerprinting their components’ unique physicochemical properties. In complex biological systems however, this can yield highly overlapping spectra that hinder sample identification. Here, we present an artificial-nose inspired SERS fingerprinting approach wh...
Biofouling is a multibillion dollar problem in the modern world, stimulating a large research effort in developing anti-fouling surface coatings. Existing theories that attempt to explain underlying molecular mechanisms of biofilm formation and its attenuation are not consistent with experiments and focus on different aspects of the interactions. T...
Molecular level insight into the interplay between protein sequence, structure, and conformational dynamics is crucial for the comprehensive understanding of protein folding, misfolding, and aggregation phenomena that are pertinent to the formation of amyloid fibrils implicated in several degenerative diseases. Computational modelling provides insi...
Metal-phenolic networks (MPNs) have received widespread interest owing to their modular incorporation of functional metal ions and phenolic ligands. However, the interaction between MPNs and biomolecules is still relatively unexplored. Herein, we studied the effects of MPN-coated gold nanoparticles on amyloid fibril formation (which is associated w...
Understanding the self-organization and structural transformations of molecular ensembles is important to explore the complexity of biological systems. Here, we illustrate the crucial role of cosolvents and solvation effects in thermodynamic and kinetic control over peptide association into ultrathin Janus nanosheets, elongated nanobelts, and amylo...
Preventing biological contamination (biofouling) is key to successful development of novel surface and nanoparticle-based technologies in the manufacturing industry and biomedicine. Protein adsorption is a crucial mediator of the interactions at the bio – nano -materials interface but is not well understood. Although general, empirical rules have b...
Quantum-sized metallic clusters protected by biological ligands represent a new class of luminescent materials; yet the understanding of structural information and photoluminescence origin of these ultrasmall clusters remains a challenge. Herein we systematically study the surface ligand dynamics and ligand-metal core interactions of peptide-protec...
The bicontinuous lipidic cubic phase (LCP), which is based on the fundamental structure of the lipid bilayer, is increasingly used in a range of applications including drug delivery, in meso crystallisation of membrane proteins, in biosensors, and in biofuel cells. The majority of LCPs investigated to date have been formulated from a single lipid o...
Nanostructured materials have great potential as platforms for analytical assays and catalytic reactions. Herein, we report the synthesis of electrocatalytically active cobalt phosphate nanostructures (CPNs) using a simple, low-cost, and scalable preparation method. The electrocatalytic properties of the CPNs toward the electrooxidation of glucose...
Hydrophilic surface chemistries can strongly bind water to produce surfaces that are highly resistant to protein adsorption and fouling. The interfacial bound water and its distinct properties have intrigued researchers for decades yet the relationship between the water three-dimensional structure and function in antifouling coatings remains elusiv...
Graphitic nanoparticles, specifically, graphene oxide (GO) nanoflakes, are of major interest in the field of nanotechnology, with potential applications ranging from drug delivery systems to energy storage devices. These applications are possible largely because of the properties imparted by various functional groups attached to the GO surface by r...
Peptide self-assembly represents a powerful bottom-up approach to the fabrication of new nanomaterials. β3-peptides are non-natural peptides composed entirely of β-amino acids, which have an extra methylene in the backbone and we reported the first fibers derived from the self-assembly of β3-peptides that adopt unique 14-helical structures. β3-pept...
Human apolipoprotein (apo) C‐II is one of several plasma apolipoproteins that form amyloid deposits in vivo and is an independent risk factor for cardiovascular disease. Lipid‐free apoC‐II readily self‐assembles into twisted‐ribbon amyloid fibrils but forms straight, rod‐like amyloid fibrils in the presence of low concentrations of micellar phospho...
The diffusion of protons along biological surfaces and the interaction of biological structures with water are fundamental areas of interest in biology and chemistry. Here, we examine the surface of insulin amyloid fibrils and follow the binding of small molecules (photoacids) that differ according to the number and location of their sulfonic group...
Self-organized bacteria have been the subject of interest for a number of applications, including the construction of microbial fuel cells. In this paper, we describe the formation of a self-organized, three-dimensional network that is constructed using Gluconobacter oxydans B-1280 cells in a hydrogel consisting of poly(vinyl alcohol) (PVA) with N-...
Complex solvation phenomena, such as specific ion effects, occur in polar liquids. Interpretation of these effects in terms of structure and dispersion forces will lead to a greater understanding of solvation. Herein, using molecular dynamics, we probe the structure of polar liquids through specific dipolar pair correlation functions that contribut...
Although several computational modelling studies have investigated the conformational behaviour of inherently disordered protein (IDP) amylin, discrepancies in identifying its preferred solution conformations still exist between various forcefields and sampling methods used. Human islet amyloid polypeptide has long been a subject of research, both...
Clustering structures from TIP3SP simulations.
The most favourable conformations and their population determined from clustering analysis over the last 50 ns (MD) and last 5 ns (REST2) of the CHARMM22* and CHARMM27 simulations with the TIP3SP water model. The protein secondary structure is represented as cartoon with the α-helix coloured in purple,...
Free energy calculations for human amylin.
This was illustrated as a function of α and β RMSD for each of the forcefields investigated in this study starting from the folded conformation. REST2 free-energy plots are on the left-hand side, and MD free-energy plots are on the right hand side.
(DOCX)
Average number of residues showing each secondary structure element.
This is determined on the equilibrated period of the folded REST2 simulations for each forcefield. §Data taken from Zerze et al. (4) §§Data taken from Hoffman et al (5).
(DOCX)
Secondary structure calculations for (A) MD and (B) REST2 simulation runs conducted with the modified TIP3SP water model. The average number of residues showing each secondary structure element determined over the equilibrated period.
(DOCX)
Metal–phenolic networks (MPNs) are a versatile class of self-assembled materials that are able to form functional thin films on various substrates with potential applications in areas including drug delivery and catalysis. Different metal ions (e.g., FeIII, CuII) and phenols (e.g., tannic acid, gallic acid) have been investigated for MPN film assem...
New aromatic molecule–seed particle interactions are examined and exploited to control and guide seed-mediated gold nanorod (Au NR) growth. This new approach enables better understanding of how small molecules impact the synthesis of metallic nanostructures, catalyzing their use in various biomedical applications, such as plasmonic biosensing. Expe...
The apolipoprotein family is structurally defined by amphipathic α-helical regions that interact with lipid surfaces. In the absence of lipid, human apolipoprotein (apo) C-II also forms well-defined amyloid fibrils with cross-β structure. Formation of this β-structure is accompanied by the burial of two charged residues, K30 and D69 that form an io...
A comprehensive understanding of the mechanisms of interaction between proteins or peptides and nanomaterials is crucial for the development of nanomaterial-based diagnostics and therapeutics. In this work, we systematically explored the interactions between citrate-capped gold nanoparticles (AuNPs) and islet amyloid polypeptide (IAPP), a 37-amino...
The organized assembly of particles into superstructures is typically governed by specific molecular interactions or external directing factors associated with the particle building blocks, both of which are particle-dependent. These superstructures are of interest to a variety of fields because of their distinct mechanical, electronic, magnetic an...
Mobile phone subscriptions continue to increase across the world, with the electromagnetic fields (EMF) emitted by these devices, as well as by related technologies such as Wi-Fi and smart meters, now ubiquitous. This increase in use and consequent exposure to mobile communication (MC)-related EMF has led to concern about possible health effects th...
Apolipoproteins form amphipathic helical structures that bind lipid surfaces. Paradoxically, lipid-free apolipoproteins display a high propensity to form cross-β structure and self-associate into disease-related amyloid fibrils. Studies of apolipoprotein C-II (apoC-II) amyloid fibrils suggest that a K30-D69 ion-pair accounts for the dual abilities...
Gold nanoparticles (AuNPs) are an integral part of many exciting and novel biomedical applications, sparking the urgent need for a thorough understanding of the physicochemical interactions occurring between these inorganic materials, their functional layers, and the biological species they interact with. Computational approaches are instrumental i...
A lack in the detailed understanding of mechanisms through which proteins adsorb or are repelled at various solid/liquid interfaces limits the capacity to rationally design and produce more sophisticated surfaces with controlled protein adsorption in both biomedical and industrial settings. To date there are two main approaches to achieve anti biof...
Gold nanoparticles (AuNPs) are an integral part of many exciting and novel biomedical applications, sparking the urgent need for a thorough understanding of the physicochemical interactions occurring between these inorganic materials, their functional layers, and the biological species they interact with. Computational approaches are instrumental i...
Electromagnetic fields (EMFs) are ever-present, and so is the need to better understand their influence on human health and biological matter in general. The interaction between a molecular system and external EMF can alter the structure, and dynamical behaviour, and, hence, biological function of proteins with uncertain health consequences. This u...
The class I hydrophobin EAS is part of a family of small, amphiphilic fungal proteins best known for their ability to self-assemble into stable monolayers that modify the hydrophobicity of a surface to facilitate further microbial growth. These proteins have attracted increasing attention for industrial and biomedical applications, with the aim of...
Responsive surfaces have been suggested to enhance longevity and antifouling performance of materials in many applications from industrial coatings to tissue engineering and drug delivery. We present a molecular dynamics study investigating de-swelling and swelling of some of the most commonly used responsive materials – PEG-functionalised silica a...
HIV-1 protease is a key enzyme in the life cycle of HIV/AIDS, as it is responsible for the formation of the mature virus particle. We demonstrate here that phage-display peptides raised against this enzyme can be used as peptide sensors for the detection of HIV-1 protease in a simple, one-pot assay. The presence of the enzyme is detected through an...
The layer-by-layer (LbL) technique is a simple and robust process for fabricating functional multilayer thin films. Here, we report the use of de novo designed polypeptides that self-assemble into coiled-coil structures (four-helix bundles) as a driving force for specific multilayer assembly. These pH- (sensitive between pH 4 and 7) and enzyme-resp...
Plasma apolipoproteins form amphipathic α-helices in lipid environments but in the lipid-free state show a high propensity to form β structure and self-associate into amyloid fibrils. The widespread occurrence of apolipoproteins in amyloid plaques suggests disease-related roles, specifically in atherosclerosis. To reconcile the dual abilities of ap...
In this study, by using X-ray powder diffraction profiles as blueprints, we successfully mapped the most probable molecular-level structural arrangement of the PMMA super-helix stereocomplexes through molecular dynamic simulations. Molecular-level resolution of the PMMA triple-helix supramolecule was not previously achievable by experimental method...
We demonstrate the direct dry transfer of large area Chemical Vapor Deposition graphene to several polymers (low density polyethylene, high density polyethylene, polystyrene, polylactide acid and poly(vinylidenefluoride-co-trifluoroethylene) by means of only moderate heat and pressure, and the later mechanical peeling of the original graphene subst...
A single-step gold nanoparticle (AuNP)-based immunoassay is demonstrated in which the nanoparticle surface is tagged with short viral peptide epitopes. Antiviral antibodies with monoclonal specificity trigger nanoparticle aggregation yielding a colorimetric response that enables detection of antibodies in the low-nanomolar range within a few minute...
Functionalizing nanoparticles with cell-penetrating peptides is a popular choice for cellular delivery. We investigated the effects of TAT peptide concentration and arrangement in solution on functionalized nanoparticles' efficacy for membrane permeation. We found that cell internalization correlates with the positive charge distribution achieved p...
The novel duolayer system, comprising a monolayer of ethylene glycol monooctadecyl ether (C18E1) and the water-soluble polymer poly(vinyl pyrrolidone) (PVP), has been shown to resist forces such as wind stress to a greater degree than the C18E1 monolayer alone. This paper reports all-atom molecular dynamics simulations comparing the monolayer (C18E...
Understanding, and improving, the behavior of thin surface films under exposure to externally applied forces is important for applications such as mimicking biological membranes, water evaporation mitigation and recovery of oil spills. This paper demonstrates that the incorporation of a water soluble polymer into the surface film composition, i.e....
A computational modeling methodology has been developed and employed to characterize the nanoscale wettability and anti-fouling properties of functionalised hard and deformable surfaces, with a specific focus on polyethylene glycol grafted substrates and their resistance to graphitic carbons. Empirical evidence suggests that the anti-fouling behavi...
Using all-atom classical molecular dynamics simulations, we have determined the structure of stereocomplexes composed of double-stranded helices of linear isotactic and cyclic syndiotactic poly(methyl methacrylate) in agreement with experimental X-ray diffraction data.
The potential for nanomaterials to interact with biological molecules has been under significant scrutiny, specifically, in their possible role as scaffolds for protein aggregation that can result in various amyloid diseases. Here, we employed classical molecular dynamics simulations to investigate the effects of graphitic carbon nanomaterials on t...
In this study, the stereocomplexation between a novel stereospecific cyclic vinyl polymer, that is, cyclic syndiotactic poly(methyl methacrylate) (st-PMMA), with the complementary linear isotactic (it-) PMMA was investigated. Surprising new insight into the effects of the topology (i.e., end groups), size, and tacticity of the assembling components...
In this study, the stereocomplexation between a novel stereospecific cyclic vinyl polymer, that is, cyclic syndiotactic poly(methyl methacrylate) (st-PMMA), with the complementary linear isotactic (it-) PMMA was investigated. Surprising new insight into the effects of the topology (i.e., end groups), size, and tacticity of the assembling components...
Author Summary
Investigation of the effects of nanomaterials on biological systems is crucial due to the increasing exposure to nanostructured materials with the growing developments and applications of nanotechnology in everyday life. Nanoparticles have been shown to have an effect on protein structure and interfere with protein self-assembly lead...
All-atom molecular dynamics simulations and experimental characterization have been used to examine the structure and dynamics of novel evaporation-suppressing films where the addition of a water-soluble polymer to an ethylene glycol monooctadecyl ether monolayer leads to improved water evaporation resistance. Simulations and Langmuir trough experi...
Mixed monolayers of 1-octadecanol (C18OH) and ethylene glycol monooctadecyl ether (C18E1) were studied to assess their evaporation suppressing performance. An unexpected increase in performance and stability was found around the 0.5:0.5 bi-component mixture and has been ascribed to a synergistic effect of the monolayers. Molecular dynamics simulati...
Cyclic peptides are increasingly being shown as powerful inhibitors of fibril formation, and have the potential to be therapeutic agents for combating many debilitating amyloid-related diseases. One such example is a cyclic peptide derivative from the human apolipoprotein C-II, which has the ability to inhibit fibril formation by the fibrillogenic...
