Carole C Perry

Carole C Perry
Nottingham Trent University | NTU · School of Science and Technology

MA, DPhil (Oxon)

About

223
Publications
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Publications

Publications (223)
Article
Tight-binding approaches bridge the gap between force field methods and Density Functional Theory (DFT). Density Functional Tight Binding (DFTB) has been employed for a wide range of systems including proteins, clays and 2D and 3D materials. DFTB is 2-3 orders of magnitude faster than DFT, allowing calculations containing up to ca. 5000 atoms. The...
Preprint
Tight-binding approaches bridge the gap between force field methods and Density Functional Theory (DFT). Density Functional Tight Binding (DFTB) has been employed for a wide range of systems containing up to ca. 5000 atoms, and has an accuracy comparable to DFT but is 2-3 orders of magnitude faster. The efficiency of DFTB comes via pre-computed int...
Presentation
Full-text available
Understanding color of blood: perspective of quantitative Raman Microscopy
Article
We report how Raman difference imaging provides insight on cellular biochemistry in vivo as a function of sub-cellular dimensions and the cellular environment. We show that this approach offers a sensitive diagnostic to address blood biochemistry at the cellular level. We examine Raman microscopic images of the distribution of the different hemoglo...
Article
Full-text available
Protein-mediated doping of ZnO with plasmonic nanoparticles offers control over surfaces, electronic states, carrier dynamics, and spectral fingerprints. Here, we report on ZnO-nano-Au bioinorganic heterostructures prepared using a chimeric polypeptide that combines most of the ZnO-binding sequence GLHVMHKVAPPR and the gold-binding AYSSGAPPMPPF seq...
Article
To advance our understanding of the molecular biochemistry of fungi which impact cultural heritage in libraries, museums and archives we investigated the diagnostic capacity of Raman spectroscopy to identify the composition of colored chromophores of fungi on paper. In this study we explored the diagnostic capacity of resonant Raman to distinguish...
Article
A hydrophobic heptapeptide, with sequence AFILPTG, as part of a phage capsid protein binds effectively to silica particles carrying negative charge. Here, we explore the silica binding activity of the sequence as a short polypeptide with polar N and C terminals. To describe the structural changes that occur on binding, we fit experimental infrared,...
Article
Full-text available
A fundamental problem in thermodynamics is the recovery of macroscopic equilibrated interaction energies from experimentally measured single-molecular interactions. The Jarzynski equality forms a theoretical basis in recovering the free energy difference between two states from exponentially averaged work performed to switch the states. In practice...
Article
The durability and long-term success of metallic implants are enhanced through the molecular scale design of biocompatible and corrosion resistant surface coatings. To pursue this hypothesis, we have developed a new class of organic-inorganic (O-I) hybrid nanocomposite coatings based on tetramethylorthosilicate (TMOS) and γ-methacryloxypropyltrimet...
Article
Full-text available
Preparation and characterization of polariton Bose-Einstein condensates in micro-cavities of high quality are at the frontier of contemporary solid state physics. Here, we report on three-dimensional polariton condensation and confinement in pseudo-spherical ZnO microcrystals. The boundary of micro-spherical ZnO resembles a stable cavity that enabl...
Article
• The essentiality of silicon for skeletal development has been established, but the adequacy of bioavailable silicon supply in broiler diets has not been considered for 30 years, despite average daily weight gain of birds increasing by almost a third over that time. Therefore, two studies were undertaken to investigate whether modern strains of br...
Article
Full-text available
Correction for ‘Azamacrocycles and tertiary amines can be used to form size tuneable hollow structures or monodisperse oxide nanoparticles depending on the ‘M’ source’ by Graham E. Tilburey, et al. , Dalton Trans. , 2019, 48 , 15470–15479.
Article
OPCT-1 is a heterogeneous prostate cancer cell line derived from primary (rather than metastatic) disease which contains epithelial, mesenchymal and CD44high/CD24low cancer stem cell (CSC) sub-populations and from which we have previously generated and characterized stable mesenchymal (P4B6B) and epithelial (P5B3) cell sub-populations. In this cont...
Article
This paper describes novel adaptations of optically sectioned planar format assays to screen compounds for their affinities to materials surfaces. The novel platform, which we name Optical sectioned Indicator Displacement Assays (O-IDA), makes use of displaceable dyes in a format adaptable to high-throughput multi-well plate technologies. We descri...
Article
Full-text available
There is high demand for new methods to modify peptides, for application in drug discovery and biomedicine. A C-H functionalization protocol for the olefination of tryptophan residues in peptides is described. The modification is successful for Trp residues at any position in the peptide, has broad scope in the styrene coupling partner, and offers...
Article
In this study, we explore the molecular mechanisms of the stability of indigo chromophores and pigments. Assisted with density functional theory, we compare visible, infrared and Raman spectral properties of model molecules, chromophores and pigments derived from living organisms. Using indigo carmine as a representative model system, we characteri...
Article
We show that the azamacrocycle ‘cyclam’ (1,4,8,11-tetraazacyclodecane) in conjunction with a silicon catecholate ion generates novel hollow tetragonal tube-like crystalline materials [(C6H4O2)3Si][C10H26N4]·H2O, whose dimensions can be tuned according to the pH of the reaction medium. The synthesis approach was successful for both silicon and germa...
Article
Full-text available
There is an increasing demand for environmentally sustainable sourcing of ingredients for the food, pharmaceutical and supplements industries. In the case of calcium carbonate (E170) as by-products from the egg and shellfish processing industries these have the potential to be sustainably sourced. In addition to their green credentials, biogenic ca...
Article
Calcium carbonate (E170) is a common food and pharmaceutical additive/ingredient. In addition to a source of calcium, the carbonate has uses including as a colour, acidity regulator and bulking agent. Globally, a range of regulatory agencies and pharmacopoeia control the analyses and specification of additives in food, supplements, pharmaceutical s...
Article
Full-text available
Equisetum species are primitive vascular plants that benefit from the biogenesis of silica bio-organic inclusions in their tissues and participate in the annual biosilica turnover in local eco-systems. As means of Equisetum reproduction and propagation, spores are expected to reflect the evolutionary adaptation of the plants to the climatic conditi...
Article
Polypeptide based biosilica composites show promise as next generation multi-functional nano-platforms for diagnostics and bio-catalytic applications. Following identification of a strong silica binder (LDHSLHS) by phage display, we conduct structural analysis of the polypeptide at the interface with amorphous silica nanoparticles in an aqueous env...
Article
New methods for peptide modification are in high demand in drug discovery, chemical biology, and materials chemistry; methods that modify natural peptides are particularly attractive. A Pd-catalyzed, C–H functionalization protocol for the olefination of phenylalanine residues in peptides is reported, which is compatible with common amino acid prote...
Article
Diversity of photo-switching structural elements open up new opportunities in the engineering of light driven reshaping of matter, in catalysis on-click including photodynamic cancer therapy, in light sensitive transport control and in data storage. Assisted with quantum calculations we explore the photo-physical properties of novel 3,3-azothiophe...
Article
Full-text available
In this study, we assessed uptake and potential efficacy of a novel, pH neutral form of silicon supplement in vitro and using broiler chickens as a model species. In vitro bioavailability of this supplement was significantly higher than other commercial supplements tested, all of which claim available silica content. To confirm bioavailability of t...
Article
Full-text available
Metallo-oxide (MO)-based bioinorganic nanocomposites promise unique structures, physicochemical properties, and novel biochemical functionalities, and within the past decade, investment in research on materials such as ZnO, TiO2, SiO2, and GeO2 has significantly increased. Besides traditional approaches, the synthesis, shaping, structural patternin...
Article
Full-text available
Biomineralization at the organic–inorganic interface is critical to many biology material functions in vitro and in vivo. Recombinant silk–silica fusion peptides are organic–inorganic hybrid material systems that can be effectively used to study and control biologically mediated mineralization due to the genetic basis of sequence control. However,...
Article
In this contribution, the effect of silica particle size (28 and 210 nm) and surface chemistry (i.e. hydroxyl, methyl or amino groups) on peptide binding response is studied with a specific emphasis on the effect of extent of functionalization on binding. Exhaustive characterization of the silica surfaces was crucial for knowledge of the chemistry...
Article
Structural properties of bioinorganic composites are of current interest in the areas of drug delivery, bone repair and biomimetics. In such composite systems, structural analysis is enhanced when we combine methods of spectroscopy and simulation. Depending on size and shape, structural discontinuities of inorganic matter may modulate the optical r...
Article
Statement of significance: The physical and mechanical properties of proteins including silk fibroin can be modified by controlled structural change, which is regularly monitored by Fourier transform infrared spectroscopy (FTIR) by peak fitting of the amide I band. Currently there is no fixed methodology to compare and follow secondary structural...
Article
Siliceous frustules of diatom algae contain unique long-chain polyamines, including those having more than six nitrogen atoms. These polyamines participate in the formation of the siliceous frustules of the diatoms but their precise physiological role is not clear. The main hypotheses include formation of a polyamine and polyphosphate supramolecula...
Article
Porous silica-based materials are attractive for biomedical applications due to their biocompatibility and biodegradable character. In addition, inorganic supports such as porous silicon are being developed due to integrated circuit chip compatibility and tunable properties leading to a wide range of multidisciplinary applications. In this contribu...
Article
Full-text available
We present a non-destructive analytical calibration tool to allow quantitative assessment of individual calcium phosphates such as hydroxyapatite (HAP) from mixtures including brushite. Many experimental approaches are used to evaluate the mineralising capabilities of biomolecules including peptides. However, it is difficult to quantitatively compa...
Article
Background: Although the popularity of using combinatorial display techniques for recognising unique peptides having high affinity for inorganic (nano) particles has grown rapidly, there are no systematic reviews showcasing current developments or patents on binding peptides specific to these materials. In this review, we summarize and discuss rec...
Article
The statement of significance: Organic-inorganic interfaces are integral to biomaterial functions in many areas of repair and regeneration. Several protein polymers have been investigated for this purpose. Despite their success the limited options to fine-tune their material properties, degradation patterns and functionalize them for each specific...
Article
Full-text available
Correction for ‘Influence of silk–silica fusion protein design on silica condensation in vitro and cellular calcification’ by Robyn Plowright et al., RSC Adv., 2016, 6, 21776–21788.
Article
The article explores the theory of infrared–visible sum frequency generation microscopy of phospholipid envelopes with dimensions larger than the wavelength of the nonlinear emission. The main part of the study concerns derivation and accounting for the contributions of effective nonlinear responses specific to sites on the surfaces of a bilayer en...
Article
A major barrier to the systematic improvement of biomimetic peptide-mediated strategies for the controlled growth of inorganic nanomaterials in environmentally benign conditions lies in the lack of clear conceptual connections between the sequence of the peptide and its surface binding affinity, with binding being facilitated by non-covalent intera...
Article
Biomaterial design via genetic engineering can be utilized for the rational functionalization of proteins to promote biomaterials integration and tissue regeneration. Spider silk has been extensively studied for its biocompatibility, biodegradability and extraordinary material properties. As a protein-based biomaterial, recombinant DNA derived deri...
Article
Full-text available
Silica is the second most abundant biomineral being exceeded in nature only by biogenic CaCO3. Many land plants (such as rice, cereals, cucumber, etc.) deposit silica in significant amounts to reinforce their tissues and as a systematic response to pathogen attack. One of the most ancient species of living vascular plants, Equisetum arvense is also...
Article
A correction of Figures 8 and 9 in the original manuscript is presented (Figures 8 and 9). Corrections are essential for Figure 8 while Figure 9 is only marginally affected and included for completeness.
Article
Cell and tissue culture has evolved from the use of simple glassware for the propagation of cells and tissues into a comprehensive platform for interrogating complex biological systems, directing cell fate, and deriving products with clinical and therapeutic value. However, despite significant advances, current in vitro culture approaches remain li...
Article
Full-text available
PDMPO (2-(4-pyridyl)-5-((4-(2-dimethylaminoethylaminocarbamoyl)methoxy)phenyl)oxazole), has unique silica specific fluorescence and is used in biology to understand biosilicification. This 'silicaphilic' fluorescence is not well understood nor is the response to local environmental variables like solvent and pH. We investigated PDMPO in a range of...
Article
Spiders spin their silk from an aqueous solution to a solid fiber in ambient conditions. However, to date the assembly mechanism in the spider silk gland has not been satisfactorily explained. In this paper, we use molecular dynamics simulations to model N. clavipes MaSp1 dragline silk formation under shear flow and determine the secondary structur...
Article
Whilst material specific peptide binding sequences have been identified using a combination of combinatorial methods and computational modelling tools, a deep molecular level understanding of the fundamental principles through which these interactions occur and in some instances modify the morphology of inorganic materials is far from being fully r...
Article
Full-text available
Biomolecule-mediated synthesis is fascinating in terms of the level of control and the intricate hierarchical structures of the materials that can be produced. In this study we compare the behavior of a phage display identified peptide, EAHVMHKVAPRP (EM 12) with that of a mutant peptide EAHVCHKVAPRP (EC-12), having additional complexation capabilit...
Article
Material binding peptides are proving to have great potential in improving material synthesis and advancing device fabrication, however, their specificity and interaction mechanisms with target surfaces remain largely elusive. This study contributes to the developing understanding of fundamental principles through which ZnO binding peptides (ZnO-BP...
Article
Developing materials that can preferentially select defined cancer cell populations for biological characterization will greatly enhance our understanding of cancer cell growth, differentiation, and invasion. The transitional events between epithelial and mesenchymal phenotypes are particularly crucial, as primary tumors and secondary metastasis ar...
Article
Bombyx mori (BM) silk fibroin is composed of two different subunits; heavy chain and light chain fibroin linked by a covalent disulphide bond. Current methods of separating the two silk fractions is complicated and produces inadequate quantities of the isolated components for the study of the individual light and heavy chain silks with respect to n...
Article
In the present study, an artificial spider silk gene, 6mer, derived from the consensus sequence of Nephila clavipes dragline silk gene, was fused with different silica-binding peptides (SiBPs) A1, A3 and R5 to study the impact of the fusion protein sequence chemistry on silica formation and the ability to generate composite silk-silica in two diffe...
Article
Full-text available
The biocompatibility and life of metallic implants can be enhanced through improving the biocompatibility and corrosion protection characteristics of the coatings used with these materials. In this study, triethylphosphite (TEP) was used to introduce phosphorus into organic-inorganic hybrid silica based sol-gel coatings prepared using γ-methacrylox...
Article
Full-text available
We demonstrate the use of silk based proteins to control the particle/crystallite size during GeO2 formation, using a bio-mimetic approach at circumneutral pH and ambient temperature. Multicrystalline GeO2 was prepared from germanium tetraethoxide (TEOG) in the presence of different silk-based proteins: Bombyx mori silk (native silk) and two chimer...
Article
Silica nanostructures are biologically available and find wide applications for drug delivery, catalysts, separation processes, and composites. However, specific adsorption of biomolecules on silica surfaces and control in biomimetic synthesis remain largely unpredictable. In this contribution, the variability and control of peptide adsorption on s...
Article
Full-text available
Under normal conditions the detachment of anchorage-dependant cells from their extracellular matrix typically induces programmed cell death which is mediated through a pathway referred to as anoikis. However, a resistance to anoikis in cancer enables the migration of cells from the primary tumour and the establishment of aggressive metastatic disea...
Article
The controlled synthesis of ZnO at the micro- and nanoscale has been the focus of significant research due to its importance in electrical and optoelectronic applications, and the potential of tuning its properties at the crystal formation stage. We present a detailed study of ZnO growth processes which supports and consolidates previous findings a...
Article
Porous materials display interesting transport phenomena due to restricted motion of fluids within the nano- to microscale voids. Here, we investigate how liquid wetting in highly ordered inverse opals is affected by anisotropy in pore geometry. We compare samples with different degrees of pore asphericity and find different wetting patterns depend...
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Full-text available
Application of novel organic-inorganic hybrid sol-gel coatings containing dispersed hydroxyapatite (HAp) particles improves the biocompatibility, normal human osteoblast (NHOst) response in terms of osteoblast viability and adhesion of a Ti6Al4V alloy routinely used in medical implants. The incorporation of HAp particles additionally results in...
Data
Silica nanostructures find applications in drug delivery, catalysis, and composites, however, understanding of the surface chemistry, aqueous interfaces, and biomolecule recognition remain difficult using current imaging techniques and spectroscopy. A silica force field is introduced that resolves numerous shortcomings of prior silica force fields...
Article
Using self-assembly, nanoscale materials can be fabricated from the bottom up. Opals and inverse opals are examples of self-assembled nanomaterials made from crystallizing colloidal particles. As self-assembly requires a high level of control, it is challenging to use building blocks with anisotropic geometry to form complex opals, which limits the...
Article
The variety of interactions that can occur at the silica/aqueous interface make silica nanoparticles (SiNPs) attractive materials for technological applications. Despite their importance, interfacial interactions are not fully understood. In this contribution we investigate the effect of: 1) particle size, and 2) surface functionalization; on the a...
Article
Interactions between peptides and proteins with material surfaces are fundamental to a broad range of applications in biotechnology and biomedical engineering. Many different methods have been developed to measure a range of properties that quantify these types of interactions. In this chapter, three of these methods are presented for the determina...
Article
In this contribution we report the unusual behavior of two peptides (Ti-1 (QPYLFATDSLIK) and Ti-2 (GHTHYHAVRTQT)) with high affinity for titania that not only efficiently promote titania mineralization from an aqueous titanium bisammonium lactatodihydroxide (TiBALDH) solution, but also effectively control the morphology and size of the precipitates...
Article
Full-text available
Nanomaterials have been the object of intense study due to promising applications in a number of different disciplines. In particular, medicine and biology have seen the potential of these novel materials with their nanoscale properties for use in diverse areas such as imaging, sensing and drug vectorisation. Gold nanoparticles (GNPs) are considere...
Article
Full-text available
The process of biofouling of marine structures and substrates, such as platforms or ship hulls, proceeds in multiple steps. Soon after the formation of an initial conditioning film, formed via the adsorption of organic particles to natural or man-made substrates, a population of different bacterial taxa associates under the formation of a biofilm....