New Publications are available for Biomolecular interactions, charge transfer complexes
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New Publications are available now online for this publication.
Please follow the links to view the publication.Temporal gene interaction regulatory networks model using temporal relation rules and 3D cube mining
http://dl-live.theiet.org/content/conferences/10.1049/ic.2009.0052
Collection of DNA segments in a cell which interact with each other and with other substances in the cell is called Gene Regulatory Networks (GRNs). The previous GRNs cannot identify the regulatory relationships according to time-varying nature, because previous methods just found the genes' relationship in the same class of molecular actions. Hence, in this paper, we propose a method for constructing a gene regulatory network that can identify the temporal regulatory relationships using time-sample-gene 3D microarray data. Firstly, the binary discretization is applied to public cell cycle-regulated Yeast Saccharomyces cerevisiae microarray dataset for representing different gene expression levels. Next, 3D cube mining directly discovers time-sample-gene 3D frequent closed patterns from 3D microarray dataset. Lastly, we build up the gene regulatory network by applying temporal relation rules to time-sample-gene patterns generated from cube mining step for detecting interaction relationship among genes. In the experiment, we vary the parameters for the method, and study these parameters' effect to the number of the generated rules. In summary, we are able to efficiently find out interactions among genes along a timeline through our research. (4 pages)Resonant acoustic profiling
http://dl-live.theiet.org/content/conferences/10.1049/ic_20060429
The article consists of a Powerpoint presentation on resonant acoustic profiling technology. The areas discussed include: components of RAP technology; antibody specificity; mouse IgG concentration analysis; IL-1β detection and interaction; serum detection; cell expression media; multi-protein complex formation; drug-enzyme profiling; kinetics of drug binding; bacteria detection; inflammatory marker; etc.Direct adsorption of chemically modified biomolecules onto gold: a rapid method for biological functionalization of MEMS
http://dl-live.theiet.org/content/conferences/10.1049/ic_20060453
The present work reports a simple, rapid and versatile strategy for glycoprotein immobilization, based on the targeted functionalization of carbohydrate residues with disulphide "anchors" derivatives able to spontaneously chemisorb onto gold, with no need of surface pre-functionalization. Different glycoproteins as enzymes and antibodies were chemically modified using this "one step" bio-immobilization protocol and directly adsorbed onto gold coated interfaces. Surface plasmon resonance (SPR) and Electrochemistry techniques revealed that direct adsorption of a modified glyco-enzyme (horseradish peroxidase) onto gold led to the formation of a densely packed SAM, where each single biomolecule is several thousand times more active than a non modified one. In the case of antibodies, the specific location of the carbohydrate moieties in the constant region resulted in the formation of active and site-oriented SAMs. This bio- immobilization method was applied to the bio- functionalization of a degenerate mode MEMS sensor (MEMSens). Preliminary results obtained for the detection of protein S-100ββ (brain injury marker), indicate a promising low detection limit.Simulation of mRNA diffusion in the nuclear environment
http://dl-live.theiet.org/content/journals/10.1049/iet-syb.2011.0032
A mathematical model is devised to study the diffusion of mRNA in the nucleus from the site of synthesis to a nuclear pore where it is exported to the cytoplasm. This study examines the role that nuclear structure can play in determining the kinetics of export by considering models in which elements of the nuclear skeleton and confinement by chromatin direct the mRNA movement. As a rule, a dense chromatin layer favours rapid export by reducing the effective volume for diffusion. However, it may also result in a heavy tail in the export time distribution because of the low mobility of molecules that accidentally find their way deep into the dense layer. An anisotropic solid-state transport system can also assist export. There exist both an optimal ratio of the anisotropy and an optimal depth of the solid-state transport layer that favour rapid export. [Includes supplementary material]Identifying similar functional modules by a new hybrid spectral clustering method
http://dl-live.theiet.org/content/journals/10.1049/iet-syb.2010.0066
Recently, a large number of researches have focused on finding cellular modules within protein–protein interaction networks. Until now, most of the works have concentrated on finding small modules and protein complexes. The authors have extended the concept of functional module and have identified larger functional modules which are the most similar to the entire network. To this end, a new hybrid spectral-based method is proposed here. First, the original graph is transformed into a line graph. Next, the nodes of the new graph are represented in the Euclidean space by using spectral methods and finally, a self-organising map is applied to the points in the new feature space. The experimental results show that similar modules, obtained from the proposed method, have own local hubs and lots of significant functional subunits concerning each other. These modules not only detect general biological processes that each protein is involved in, but also due to great similarities to the original network, it can be used as significant subnetworks for predicting protein function as detailed as possible. Some interesting properties of these modules are also investigated in this research. [Includes supplementary material]Protein–gold nanoparticles interactions and its application for alkaline phosphatase assay
http://dl-live.theiet.org/content/journals/10.1049/mnl.2012.0455
Proteins-modified gold nanoparticles (AuNPs) have been considered as attractive materials in many fields especially in biosensing. In this Letter, the authors have studied the relationship between ratios of specific amino acids and protein–AuNPs interactions. A new indicator <i xmlns="http://pub2web.metastore.ingenta.com/ns/">R</i><sub xmlns="http://pub2web.metastore.ingenta.com/ns/">w/s</sub>, calculated from the ratios of certain hydrophilic amino acids, is proposed to reveal the affinity coefficient between proteins and AuNPs. Experimental results show that the proposed <i xmlns="http://pub2web.metastore.ingenta.com/ns/">R</i><sub xmlns="http://pub2web.metastore.ingenta.com/ns/">w/s</sub> can indicate the binding status of proteins and AuNPs effectively. The authors have also introduced alkaline phosphatase, a protein with relatively low <i xmlns="http://pub2web.metastore.ingenta.com/ns/">R</i><sub xmlns="http://pub2web.metastore.ingenta.com/ns/">w/s</sub>, for detection by the colorimetric shift based on strong protein–AuNPs interactions.Enhanced gene transfer with multilayered polyplexes assembled with layer-by-layer technique
http://dl-live.theiet.org/content/journals/10.1049/iet-nbt.2011.0031
Successful gene therapy asks for multifunctional vectors which can not only protect DNA from degradation but also transfer it into nuclear and subsequently express the loaded gene. Here we reported a novel multilayered delivery system constructed with DNA, protamine (Pro) and polyethylenimine (PEI) via lay-by-layer (LbL) technique, which posed multifunctions. DNA was previously condensed into a compact core with Pro which also contained nuclear localisation signals (NLS) domains for nuclear transfer. Then additional DNA was deposited as the first layer onto the cationic core via the electrostatic attraction which would increase the loading dose of DNA. At last, PEI was absorbed as the outmost layer to achieve the endosomal escape. Therefore a quaternary polyplexes which offered high loading of DNA, nuclear transfer ability and endosomal escape capability was constructed with the LbL technique. The obtained quaternary polyplexes showed positive surface charge, spherical morphology, a relatively narrow particle size distribution and strong DNA protection capability. Compared with commercially available PEI/DNA complexes, the novel multifuctional vector exhibited not only lower cytotoxicity (<i xmlns="http://pub2web.metastore.ingenta.com/ns/">P</i><0.05) but also higher transfection efficiency in HepG2 and HeLa cells (<i xmlns="http://pub2web.metastore.ingenta.com/ns/">P</i><0.05) in vitro test.Immobilisation of cobaltferritin onto gold electrode based on self-assembled monolayers
http://dl-live.theiet.org/content/journals/10.1049/iet-nbt.2011.0042
The iron storage protein, ferritin, has a cavity of ∼7 nm in diameter in which iron is oxidised and stored as a hydrated oxide core. Electron transfer is known to be an important step in the sequestering of iron by cellular ferritin. The cavity was used as a nanocontainer to grow cobalt nanoparticles. The immobilisation of ferritin on the electrode surface is essential for various bioelectronic applications. A cobaltferritin-immobilised electrode based on self-assembled monolayer (SAM)-modified gold electrode was developed. The cobaltferritin-immobilised SAM-modified electrode was characterised by electrochemical and atomic force microscopy (AFM) techniques. The results indicated that cobaltferritin was selectively immobilised onto succinimidyl alkanedisulfide-modified Au electrode by the covalent interaction between cobaltferritin and the terminal functional groups of the SAMs. The cobaltferritin immobilised modified electrode showed a direct electron transfer reaction between cobaltferritin and the electrode. The electrochemically regulated uptake and release of cobalts for cobaltferritin immobilised on the SAMs were demonstrated. The results obtained in this study indicate that cobaltferritin has potential for a biomaterial in nanoscale synthesis for potential magnetic, catalytic and biomedical-sensing applications.Dynamic modelling of protein and oxidative metabolisms simulates the pathogenesis of Parkinson's disease
http://dl-live.theiet.org/content/journals/10.1049/iet-syb.2011.0075
Research into Parkinson's disease (PD) is difficult and time consuming. It is a complex condition that develops over many decades in the human brain. For such apparently intractable diseases, mathematical models can offer an additional means of investigation. As a contribution to this process, the authors have developed an ordinary differential equation model of the most important cellular processes that have been associated with PD. The model describes the following processes: (i) cellular generation and scavenging of reactive oxygen species; (ii) the possible damage and removal of the protein α-synuclein and, (iii) feedback interactions between damaged α-synuclein and reactive oxygen species. Simulation results show that the Parkinsonian condition, with elevated oxidative stress and misfolded α-synuclein accumulation, can be induced in the model by known PD risk factors such as ageing, exposure to toxins and genetic defects. The significant outcome of the paper is the demonstration that it is possible to reproduce <i xmlns="http://pub2web.metastore.ingenta.com/ns/">in silico</i> the multi-factorial interactions that characterise the pathogenesis of PD. As such, the model provides a systematic explanation of the variability and heterogeneity of PD and provides the basis for computational studies of further facets of this complex multi-factorial condition. [Includes supplementary material]Lateral field excited film bulk acoustic resonator for detection of protein–ligand interactions
http://dl-live.theiet.org/content/journals/10.1049/el.2012.2156
Presented is a lateral field excited film bulk acoustic resonator for real-time sensing of protein–ligand interaction using the biotin–streptavidin system as a model. The film bulk acoustic resonator works at 2 GHz in shear mode. For biosensing, the biotin was immobilised on one face of the resonator as the probe. The resonant frequency of the biotin-immobilised device drops rapidly at first and gradually reaches equilibrium when exposed to the streptavidin solutin due to the biotin–streptavidin interaction. Consequently, the lateral field excited film bulk acoustic resonator can be used to study the kinetics of protein–ligand interaction without the use of labelling or molecular tags. The proposed device shows promising applications for disease diagnostics, prognosis, and drug discovery.Photoresist functionalisation method for high-density protein microarrays using photolithography
http://dl-live.theiet.org/content/journals/10.1049/mnl.2012.0336
Since the last decade, there is a growing need for patterned biomolecules for various applications ranging from diagnostic devices to enabling fundamental biological studies with high throughput. Protein arrays facilitate the study of protein–protein, protein–drug or protein–DNA interactions as well as highly multiplexed immunosensors based on antibody–antigen recognition. Protein microarrays are typically fabricated using piezoelectric inkjet printing with resolution limit of ∼70–100 µm limiting the array density. A considerable amount of research has been done on patterning biomolecules using customised biocompatible photoresists. Here, a simple photolithographic process for fabricating protein microarrays on a commercially available diazo-naphthoquinone-novolac-positive tone photoresist functionalised with 3-aminopropyltriethoxysilane is presented. The authors demonstrate that proteins immobilised using this procedure retain their activity and therefore form functional microarrays with the array density limited only by the resolution of lithography, which is more than an order of magnitude compared with inkjet printing. The process described here may be useful in the integration of conventional semiconductor manufacturing processes with biomaterials relevant for the creation of next-generation bio-chips.Microfluidic approach to genotyping human platelet antigens
http://dl-live.theiet.org/content/journals/10.1049/iet-nbt.2011.0044
Centralised laboratories routinely determine blood types by serological and molecular methods. Current practices have limitations in terms of cost, time and accessibility. Miniaturised microfluidic platforms offer an alternative to conventional genotyping methods, since they consume fewer reagents, provide faster analysis and allow for complete integration and automation. As these ‘lab-on-a-chip’ devices have been used for bacterial and viral detection, the authors investigated blood group genotyping as a novel application of microfluidic technology. To demonstrate the feasibility of microfluidic chip-based genotyping, the authors compared human platelet antigen 1 (HPA-1) genotype results from conventional and chip-based analysis for 19 blood donor specimens. DNA purification was performed with ChargeSwitch™ magnetic beads, DNA amplification (PCR), restriction length polymorphism (RFLP) and capillary electrophoresis (CE) for identification of the DNA on microfluidic chips. It was found that nine donors were HPA-1a/1a and ten were HPA-1a/1b. Concordance between the conventional and on-chip methods was achieved for all but one sample. All the steps were demonstrated for complete blood group genotyping analysis of patient whole blood specimens on separate microfluidic chips. Future work will focus on integration of all the genotyping protocols on a single microfluidic chip.Immobilisation of heparin on bacterial cellulose-chitosan nano-fibres surfaces via the cross-linking technique
http://dl-live.theiet.org/content/journals/10.1049/iet-nbt.2011.0038
In recent years, bacterial cellulose (BC) has been fabricated in tubular shape as scaffold for vascular tissue engineering. However, in order to improve the blood compatibility and regenerative ability of BC, BC nano-fibres should be cross-linked with some materials which can prevent the formation of blood clot. In this work, a novel BC–chitosan (CS)/heparin (Hep) composite was prepared. Scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD) and Fourier-transformed infrared spectroscopy (FTIR) were used to analyse the obtained samples. It is observed by SEM and TEM that the obtained composites remain the three-dimensional (3D) network and porous structure. The results of XRD reveal that the curve of BC–CS/Hep composite assumes the characteristic absorption peaks of BC, CS and Hep. The FTIR results also confirm the presence of CS and Hep on the surface of BC nano-fibres. In conclusion, BC–CS/Hep composites were obtained by the co-synthesis technique and the cross-linking method, respectively. Furthermore, the MC3T3-E1 cells were seeded on the obtained samples to test the cell compatibility. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide results indicated that the BC–CS/Hep composites were suitable for cell proliferation and ingrowth.Force–velocity relationship of single actin filament interacting with immobilised myosin measured by electromagnetic technique
http://dl-live.theiet.org/content/journals/10.1049/ip-nbt_20045003
The effect of applying an external load to actin filaments moving in the <i xmlns="http://pub2web.metastore.ingenta.com/ns/">in vitro</i> motility assay is studied. Bead-tailed actin filaments were made by polymerising actin onto 2.8 μm diameter Dynabeads conjugated with gelsolin-G actin. These were introduced into a motility cell coated with 100 μg/ml rabbit fast skeletal myosin in the presence of ATP and 0.5% methylcellulose. The motility cell was inserted between the pole-pieces of an electromagnet and the fluorescent beads and filaments were observed. The force–current relationship of the electromagnet was determined from the velocity of free beads in viscous solution and Stokes' equation. The magnet produced up to 6 pN force on the Dynabeads at 1 A. Many bead-tailed actin filaments stuck to the surface, but the beads that did move moved at the same speed as unloaded f-actin in the same cell. Bead-tailed filaments slowed down under an increasing magnetic load, eventually stalled and then slid backward under increasing load before detaching from the surface. Single-filament force–velocity curves were constructed and a stalling force of about 0.6 pN/mm of actin filament estimated.Molecular resolution of cell adhesion forces
http://dl-live.theiet.org/content/journals/10.1049/ip-nbt_20040707
Recently, AFM-based force spectroscopy has been used to quantify single-molecule adhesion forces on living ameboid cells. Force spectroscopy was used to measure the rupture forces of single receptor–ligand bonds which can occur rapidly between the cell types used, a metastasising B16 melanoma cell and a vascular bEnd.3 endothelial cell. Parameters which influence the critical experimental conditions are discussed to discriminate between multiple bond ruptures and single bonds. Under physiological conditions of temperature and pH the force measurements show an average rupture force of 33 pN (SD=12 pN) for single bonds. Single-molecule force spectroscopy will be very useful to study the regulation of cell adhesion on a molecular level in normal processes, such as leukocyte homing, and in major human disorders, including tumor metastasis, autoimmune diseases and atherosclerosis.Towards nanomedicine with a supramolecular approach: a review
http://dl-live.theiet.org/content/journals/10.1049/ip-nbt_20050003
A review dedicated mainly to the results obtained by the authors on the use of cyclodextrin (CD) derivatives on protein (enzyme) stabilization through covalent and non-covalent interactions (host–guest supramolecular interactions) is presented here. This latter procedure served to introduce a new method for enzyme immobilization on metallic surfaces that can be used to prepare biosensors and therapeutic nanodevices. The surfaces of gold (and silver) electrodes and nanoparticles were modified with sulphur-containing cyclodextrin derivatives. The protein (enzyme) was then supramolecularly immobilized on the modified surface when one or more of its bulky hydrophobic moieties was included into the CD cavity. The protein can also be modified with a typical CD guest, such as adamantane, to achieve a more stable immobilization. Different examples are presented, such as a biosensor based on monolayers of adamantane-modified cytochrome <i xmlns="http://pub2web.metastore.ingenta.com/ns/">c</i> and a bienzymatic nanodevice comprising gold nanoparticles stabilized with CD associated to catalase and superoxide dismutase modified with complementary host–guest residues. The possibilities of this new approach for the development of biosensors and therapeutic nanodevices are analyzed.Self-association behaviour of protein:surfactant systems in alcohol/water mixtures
http://dl-live.theiet.org/content/journals/10.1049/ip-nbt_20050006
The effect of the addition of short-chain monohydric alcohols (ethanol and propan-2-ol) to the protein:surfactant system lysozyme:sodium dodecyl sulfate (Lz:SDS) in aqueous solution was investigated using a conductometric technique. A second protein:surfactant system, bovine serum albumin:SDS (BSA:SDS) was also investigated so that the effect of a different protein conformation and composition could be compared. The critical aggregation concentration (CAC) of the protein forming the complex and the critical micelle concentration (CMC*) of SDS in the presence of protein, at different alcohol concentrations, were determined. It was found in both cases that the addition of alcohol does not produce a significant change in the CAC, whereas the CMC* displays variation with alcohol concentration that shows an inversion in the ranges 0.05–0.06 ethanol mole fraction and 0.02–0.03 propan-2-ol mole fraction. This suggests that, in contrast with the CAC behaviour, the major factor that drives SDS micellisation in the presence of protein is the variation in water structure. Results also suggest that it occurs in the same way for both proteins, where electrostatic interactions are the main force in the formation of the complex. Conversely, hydrophobic interactions play the dominant role at the micellisation stage, and only the extent of the interaction between protein:surfactant aggregates and surfactant species seems to depend on protein nature.Scanning probe technology in metalloprotein and biomolecular electronics
http://dl-live.theiet.org/content/journals/10.1049/ip-nbt_20040504
The interfacing of man-made electronic components with specifically-folded biomacromolecules lies central not only to the development of sensory interfaces and potential new molecular-scale devices, but also enables us to analyse processes of great biological importance in a refined and controllable manner. Recent advances in both available technology, most notably optical and scanning probes in nature, and our understanding of suitable methodologies, have led us to the point where the characteristics of single biological molecules can be interrogated with good levels of reproducibility. We review here the application of scanning probe microscopy to the analysis of and experimentation on biological redox systems. Within this paper the tunnel transport characteristics, as assayed by both scanning tunnelling microscopy (STM) and conducting probe atomic force microscopy (AFM), of single metalloproteins are discussed. In a specific case study the electron transfer characteristics of the blue copper metalloprotein, azurin, are reported. The modulation of these properties under the influence of calibratable compressional force has also been examined in some detail. Work such as this enables one to reproducibly establish the conductance, barrier height, environmental sensitivity and electromechanical properties of these molecules.Biomolecule-compatible support structures for biomolecule coupling to physical measuring principle surfaces
http://dl-live.theiet.org/content/journals/10.1049/ip-nbt_20040691
As part of studies on biomolecule-compatible interfacial structures for practice-relevant biosensor and biochip developments, new film-forming aminocelluloses of the ‘P-CH<sub xmlns="http://pub2web.metastore.ingenta.com/ns/">2</sub>-NH-(X)-NH<sub xmlns="http://pub2web.metastore.ingenta.com/ns/">2</sub>’ type (P=cellulose) with spacer structures (X=special oligoamine residues) at C6 and solubilising groups (S=tosylate or carbanilate) at C2/C3 of the anhydroglucose unit (AGU) were synthesised and their film properties and covalent coupling with enzyme protein examined. Depending on the nature and degree of substitution (DS<sub xmlns="http://pub2web.metastore.ingenta.com/ns/">(S)</sub>) of the ester groups (S) at C2/C3, the new aminocellulose derivatives are soluble either in DMA and DMSO (with S=carbanilate) or in water (with S=tosylate). The aminocellulose derivatives form transparent films from their solutions. AFM investigations of the film surfaces have either shown very flat (topography <1 nm) films or tubular topographies of nanostructure size, depending on structural and environment-induced factors of influence. Especially in the case of films from water-soluble aminocelluloses with oligoamine residues at C6, inter alia, enzyme-specific pH values and different positive charge distributions can be adjusted by partial protonation of the NH<sub xmlns="http://pub2web.metastore.ingenta.com/ns/">2</sub> end groups. By means of the covalent coupling of the new aminocelluloses with glucose oxidase (GOD) it was shown that the enzyme coupling efficiency can be decisively optimised by the interplay of aminocellulose structure, coupling structure and enzyme protein.Preliminary electrochemical characterisation of cytochrome P4501A2-clozapine interaction
http://dl-live.theiet.org/content/journals/10.1049/ip-nbt_20030534
Cytochromes P450 are a large superfamily of heme-thiolate enzymes involved in the metabolism of many different organic substrates such as drugs, fatty acids and toxic compounds. The aim of this work is to analyse the binding between the cytochrome P4501A2, in solution and in gel-matrix, and its substrate (clozapine), utilising voltammetric tests. The interaction measurements were carried out using two different screen printed electrodes (rhodium–graphite and graphite–riboflavin), and the results were compared. It was demonstrated that it is possible to realise a biosensor prototype to detect the presence of clozapine indirectly by chronoamperometry.Surface plasmon resonance imaging for biosensing
http://dl-live.theiet.org/content/journals/10.1049/iet-nbt.2008.0012
Surface plasmon resonance imaging (SPRI) is a useful tool for the study of surface biomolecular interactions allowing for label-free detection and elegant instrumentation. SPRI imaging system is described in this review with an emphasis on recent applications with examples of different biological interactions and high throughput analysis. Signal amplification in SPRI using nanoparticle and waveguide-based optical coupling is introduced. Finally the detection sensitivity of the SPRI system is examined in terms of other competitive methods.Synthesis of different-sized silver nanoparticles by simply varying reaction conditions with leaf extracts of <i xmlns="http://pub2web.metastore.ingenta.com/ns/">Bauhinia variegata</i> L.
http://dl-live.theiet.org/content/journals/10.1049/iet-nbt.2010.0015
Green synthesis of nanoparticles is one of the crucial requirements in today's climate change scenario all over the world. In view of this, leaf extract (LE) of <i xmlns="http://pub2web.metastore.ingenta.com/ns/">Bauhinia variegata</i> L. possessing strong antidiabetic and antibacterial properties has been used to synthesise silver nanoparticles (SNP) in a controlled manner. Various-sized SNP (20–120 nm) were synthesised by varying incubation temperature, silver nitrate and LE concentrations. The rate of SNP synthesis and their size increased with increase in AgNO<sub xmlns="http://pub2web.metastore.ingenta.com/ns/">3</sub> concentration up to 4 mM. With increase in LE concentration, size and aggregation of SNP was increased. The size and aggregation of SNP were also increased at temperatures above and below 40°C. This has suggested that size and dispersion of SNP can be controlled by varying reaction components and conditions. Polarity-based fractionation of <i xmlns="http://pub2web.metastore.ingenta.com/ns/">B. variegata</i> LE has suggested that only water-soluble fraction is responsible for SNP synthesis. Fourier transform infrared spectroscopy analysis revealed the attachment of polyphenolic and carbohydrate moieties to SNP. The synthesised SNPs were found stable in double distilled water, BSA and phosphate buffer (pH 7.4). On the contrary, incubation of SNP with NaCl induced aggregation. This suggests the safe use of SNP for various <i xmlns="http://pub2web.metastore.ingenta.com/ns/">in vivo</i> applications.Hepatitis B surface antigen–antibody interactions studied by optical tweezers
http://dl-live.theiet.org/content/journals/10.1049/iet-nbt.2010.0023
The protein–protein interactions between hepatitis B surface antigen (HBsAg) and its antibodies (anti-HBs) were studied by measuring the binding force between microspheres coated with such proteins using optical tweezers. The interaction force between the protein-coated microspheres was found to be strongly influenced by the acidity of the surrounding liquid medium, as well as the experimental temperature, and it reaches a maximum value at around pH 7.5 and temperature around 37°C. By measuring the protein distribution on the surfaces of the microspheres and their contact areas using scanning electron microscopy, the specific binding force between an HBsAg and anti-HBs protein pair is estimated to be around 4.8 pN at the optimum pH value and temperature at an applied loading rate of around 1 pN/s.Characterisation of protein adsorption on different liquid crystal phthalocyaninethin films
http://dl-live.theiet.org/content/journals/10.1049/iet-nbt.2009.0011
Bovine serum albumin (BSA) protein adsorption on thin spun films of different metal octakishexylthiophthalocyanine [(C<sub xmlns="http://pub2web.metastore.ingenta.com/ns/">6</sub>S)<sub xmlns="http://pub2web.metastore.ingenta.com/ns/">8</sub>PcM, M=Cu, Ni] derivatives is investigated by using three independent spectroscopic measurements namely Raman spectroscopy, ellipsometry and surface plasmon resonance imaging. Thermally induced molecular self-reorganisations in the phthalocyanine films are found to have produced the changes in the surface energy which, in turn, control protein adsorption. The amount of BSA adsorption on [(C<sub xmlns="http://pub2web.metastore.ingenta.com/ns/">6</sub>S)<sub xmlns="http://pub2web.metastore.ingenta.com/ns/">8</sub>PcNi] is more limited than that on [(C<sub xmlns="http://pub2web.metastore.ingenta.com/ns/">6</sub>S)<sub xmlns="http://pub2web.metastore.ingenta.com/ns/">8</sub>PcCu] and this observation is consistent with the results on the surface wettability obtained from the contact angle measurements. The shift from the plasmonic resonance wavelength because of the BSA adsorption was significantly larger for the heat-treated [(C<sub xmlns="http://pub2web.metastore.ingenta.com/ns/">6</sub>S)<sub xmlns="http://pub2web.metastore.ingenta.com/ns/">8</sub>PcCu] than as-deposited film. Similar measurements on the [(C<sub xmlns="http://pub2web.metastore.ingenta.com/ns/">6</sub>S)<sub xmlns="http://pub2web.metastore.ingenta.com/ns/">8</sub>PcNi] films showed a limited BSA adsorption. The results of surface plasmon resonance experiments are consistent with those obtained from Raman spectroscopic and ellipsometric techniques.Probing the interaction of bovine haemoglobin with gold nanoparticles
http://dl-live.theiet.org/content/journals/10.1049/iet-nbt.2011.0029
The interaction between gold nanoparticles (GNPs) and bovine haemoglobin (BHb) was studied by ultraviolet–visible (UV–Vis) absorption, circular dichroism (CD) and fluorescence spectroscopic techniques. The UV–Vis absorption spectrum demonstrated that there was interaction between GNPs and BHb, but no direct interaction between GNPs and haem groups of BHb. The fluorescence data revealed that GNPs effectively quenched the intrinsic fluorescence of BHb via static quenching. The binding of GNPs to BHb occurred at a single site. The binding process was a spontaneous molecular interaction procedure, in which hydrophobic force and hydrogen bonds played a major role. The alternations of protein secondary structure in the presence of GNPs were also determined by CD spectroscopy. This work is helpful to understand the interaction mechanism of GNPs with haemoglobin, which can guide the applications of GNPs in biomedicine.Optimal ratio of scaffold complex to free Fus3 to maximise the accumulation of phosphorylated Fus3 in yeast pheromone signalling pathway
http://dl-live.theiet.org/content/journals/10.1049/iet-syb.2011.0016
In this study, the author considers the design rule of the intracellular signalling pathway. In yeast pheromone signalling pathway, scaffold Ste5 tethers the components of signalling pathway, Ste11, Ste7 and Fus3. Even though scaffold complex is independently produced before stimuli, excessively expressed Fus3 as compared with scaffold exists in cytoplasm as free kinase. How the ratio of scaffold complex to the free Fus3 is determined is not clear yet. First, the contribution of free Fus3 to signal transduction is theoretically shown by using a simplified model of pheromone signalling pathway. Next, the optimum expression levels of Ste5, Ste11, Ste7 and Fus3 are systematically explored by using the detailed model and genetic algorithm under the constraint that the total expression level of these four genes is limited. Excessive expression of Fus3 is advantageous for the efficient signalling without stall of the signal transduction. The result suggests that the component of signalling pathway is optimally expressed to maximise the accumulation of phosphorylated Fus3 at a fixed time point under the constraint that the total gene expression is limited. The proposed model provides further insight into the signalling network from the point of view of not only its function but also its optimality.Spatial localisation of chaperone distribution in the endoplasmic reticulum of yeast
http://dl-live.theiet.org/content/journals/10.1049/iet-syb.2011.0006
In eukaryotes, the endoplasmic reticulum (ER) serves as the first membrane-enclosed organelle in the secretory pathway, with functions including protein folding, maturation and transport. Molecular chaperones, of the Hsp70 family of proteins, participate in assisting these processes and are essential to cellular function and survival. BiP is a resident Hsp70 chaperone in the ER of <i xmlns="http://pub2web.metastore.ingenta.com/ns/">Saccharomyces cerevisiae</i>. In this study the authors have created a partial differential equation model to examine how BiP interacts with the membrane-bound co-chaperone Sec63 in translocation, a process in which BiP assists in guiding a nascent protein into the ER lumen. It has been found that when Sec63 participates in translocation through localisation at the membrane, the spatial distribution of BiP is inhomogeneous, with more BiP at the surface. When translocation is inhibited through a disabling of Sec63's membrane tether, the concentration of BiP throughout the ER becomes homogeneous. The computational simulations suggest that Sec63's localisation and the resulting binding to BiP near the membrane surface of the ER enable a heterogeneous distribution of BiP within the ER, and may facilitate BiP's role in translocation. [Includes supplementary material]Growth-related model of the <i xmlns="http://pub2web.metastore.ingenta.com/ns/">GAL</i> system in <i xmlns="http://pub2web.metastore.ingenta.com/ns/">Saccharomyces cerevisiae</i> predicts behaviour of several mutant strains
http://dl-live.theiet.org/content/journals/10.1049/iet-syb.2010.0060
The genetic regulatory network responds dynamically to perturbations in the intracellular and extracellular environments of an organism. The <i xmlns="http://pub2web.metastore.ingenta.com/ns/">GAL</i> system in the yeast <i xmlns="http://pub2web.metastore.ingenta.com/ns/">Saccharomyces cerevisiae</i> has evolved to utilise galactose as an alternative carbon and energy source, in the absence of glucose in the environment. This work contains a modified dynamic model for <i xmlns="http://pub2web.metastore.ingenta.com/ns/">GAL</i> system in <i xmlns="http://pub2web.metastore.ingenta.com/ns/">S. cerevisiae</i>, which includes a novel mechanism for Gal3p activation upon induction with galactose. The modification enables the model to simulate the experimental observation that in absence of galactose, oversynthesis of Gal3p can also induce the <i xmlns="http://pub2web.metastore.ingenta.com/ns/">GAL</i> system. Subsequently, the model is related to growth on galactose and glucose in a structured manner. The growth-related models are validated with experimental data for growth on individual substrates as well as mixed substrates. Finally, the model is tested for its prediction of a variety of known mutant behaviours. The exercise shows that the authors’ model with a single set of parameters is able to capture the rich behaviour of the <i xmlns="http://pub2web.metastore.ingenta.com/ns/">GAL</i> system in <i xmlns="http://pub2web.metastore.ingenta.com/ns/">S. cerevisiae.</i> [Includes supplementary material]Surface functionalisation of magnetic nanoparticles: quantification of surface to bulk amine density
http://dl-live.theiet.org/content/journals/10.1049/mnl.2010.0112
Work has been conducted to adapt a colourimetric assay previously used on flat surfaces for the assay of amine group density on nanoparticles silanised with 3-(aminopropyl) triethoxysilane. The new assay was rapid, easy to perform, and linear in the range of optical density (OD<sub xmlns="http://pub2web.metastore.ingenta.com/ns/">282 nm</sub>) values of 0.080–1.6 for particle suspension densities of between 0.5 and 7.0 mg/ml. In addition, the same materials, as well as the ones activated using 3-(aminopropyl) diethoxy methyl silane, were investigated for their elemental compositions by, combustion carbon-hydrogen-nitrogen (CHN) analysis and results from both approaches together have permitted the accurate calculation of the ratio of surface to total amine density for the materials when activated in water. This value can in turn be used as an indication of a surface amino structure (i.e. mono or multilayer). The aminosilanisation processes were further characterised by DNA-binding/elution and zeta potential measurement. This combination of approaches provides a fast, convenient and effective means of measuring surface amine densities on particles and yields information about the structure of the surface aminosilanes layers.BioFET sensor for detection of albumin in urine
http://dl-live.theiet.org/content/journals/10.1049/el_20083551
Characterisation of a BioFET for detection of albumin in a mixture of human urine is presented. To avoid electrolyte effect of the urine, it was measured in PBS (phosphate buffer saline) at a fixed pH after albumin binding. The drain current was modulated by the albumin bound to the anti-albumin immobilised on the gate surface of the BioFET. The current variation ratio was likely to be proportional to the concentration of the albumin in the range 50–250 mg/l. The results show the feasibility of the BioFET as a urinary albumin sensor.Label-free kinetic study of biomolecular interactions by white light reflectance spectroscopy
http://dl-live.theiet.org/content/journals/10.1049/mnl_20065019
Binding of biomolecules in real-time is studied by white light reflectance spectroscopy (WLRS). The experimental apparatus consists of a WLRS setup and a microfluidic channel for the supply of the biomolecules solutions placed above the sample on which the biomolecular interactions take place. Using this setup, it is possible to monitor in real-time the biomolecular film thickness changes during the binding of biomolecules on a properly treated surface. The sample is a silicon wafer with a thick thermally grown silicon dioxide (∼1044 nm) and a thin (∼35 nm) polymer layer. The proposed methodology has been applied for the monitoring of streptavidin binding to surface-immobilised biotinylated protein. The biomolecular interactions are monitored as shifts of the wavelength where constructive interference is observed. The proposed methodology provides a simple, fast, low cost approach for a label-free monitoring of biomolecular interactions.Nucleotides, RNA and DNA selective adsorption on atomic-flat Mg–Al-hydroxysilicate substrates
http://dl-live.theiet.org/content/journals/10.1049/mnl.2011.0546
The search and characterisation of new nanomaterials and their application to nanomanipulate biomolecules are modern challenges of nanoscience and nanotechnology. Both synthetic and natural materials are widely investigated. In this Letter the authors report on the interaction of fundamental biomolecules with atomic-flat natural magnesium–aluminium-hydroxysilicate substrates. The surface affinity, self-assembly and nanopatterning of nucleotides, RNA and DNA, are compared. All biomolecules selectively adsorb on the surface of the magnesium hydroxide layer. Nucleotides are lined-up at the edges of magnesium hydroxide in long filamentary structures. RNA molecules are observed as agglomerates, globular domains separated by strands, and also in stable linearised structures. DNA can be bridged between two magnesium hydroxide layers in a stretched conformation longer than 2 µm (>6000 bp).Development of capacitance measurement system for human serum albumin detection
http://dl-live.theiet.org/content/journals/10.1049/el.2010.0234
The use of interdigitated electrodes and binding with Cibacron blue F3GA by self-assembly technology, which has high affinity for human serum albumin (HSA), and serves as a receptor for HSA detection, is reported. In preliminary tests, the interdigitated chip measured the impedance of HSA by electrochemical impedance spectroscopy and this result indicated the characteristic frequency of impedance change below 1.1 kHz. However, a portable capacitance measurement system made using a standard operational amplifier circuit and AC excitation was applied at 1 kHz. The detection result showed a significant linear correlation between HSA concentration (0.1 to 1 mg/ml) and output voltage. The regression equation was Y=17.91+323.72X with R<sup xmlns="http://pub2web.metastore.ingenta.com/ns/">2</sup>=0.999. This reported study has successfully demonstrated that the capacitive sensor has great potential for applications in HSA detection.Surface plasmon resonance and immunosensors
http://dl-live.theiet.org/content/journals/10.1049/el_19840660
A rough surface analysis of surface plasmon resonance (SPR) is applied to a glass/silver/antigen/antibody/electrolyte multilayer. Comments are made on the experimental arrangements most appropriate to the development of SPR immunosensors.Protein–protein/DNA interaction networks: versatile macromolecular structures for the control of gene expression
http://dl-live.theiet.org/content/journals/10.1049/iet-syb_20080091
The assembly of macromolecular structures consisting of proteins and DNA lies at the core of many fundamental cellular processes, such as transcription, recombination and replication. A common theme to all these processes is DNA looping, which provides the backbone for the required long-range interactions on DNA and results in further complexity that is exceptionally difficult to tackle with traditional quantitative approaches. Here, recent advances in mathematical and computational methods to study the assembly of protein–protein/DNA complexes with loops and their effects in the cellular behaviour through gene regulation are reviewed. The interplay between multisite DNA looping and DNA bending regulatory proteins, such as the catabolite activator protein (CAP), and on its physiological consequences is focused on. It has become clear in the last few years that the complexity that looping brings about can actively control transcriptional noise and cell-to-cell variability. Here, it is shown that the DNA looping, through the effects of CAP, can also control the balance between robustness and sensitivity of the induction of gene expression.Computer evaluation of network dynamics models with application to cell cycle control in budding yeast
http://dl-live.theiet.org/content/journals/10.1049/ip-syb_20050029
Cellular processes are governed by complex networks of interacting genes and proteins. Theoretical molecular biologists attempt to describe these processes via mathematical models by writing biochemical reaction equations. Modellers are building increasingly larger and complex mathematical models to describe these cellular processes, making model evaluation a time consuming and difficult task. The authors describe an automatable process for model evaluation and a software system that implements this process. The software is adaptable to many types of models and is freely available along with all needed data files. The cell cycle control system for budding yeast is known in fine detail and constrained by more than 100 phenotypic observations in mutant strains. As an example, the authors apply their process to a model of cell cycle control in budding yeast containing dozens of regulatory equations and explaining nearly all of the known mutant phenotypes.Shaping the response: the role of FcεRI and Syk expression levels in mast cell signalling
http://dl-live.theiet.org/content/journals/10.1049/iet-syb.2010.0006
Many receptor systems initiate cell signalling through ligand-induced receptor aggregation. For bivalent ligands binding to mono- or bivalent receptors, a plot of the equilibrium concentration of receptors in aggregates against the log of the free ligand concentration, the cross-linking curve, is symmetric and bell shaped. However, steady state cellular responses initiated through receptor cross-linking may have a different dependence on ligand concentration than the aggregated receptors that initiate and maintain these responses. The authors illustrate by considering the activation of the protein kinase Syk that rapidly occurs after high affinity receptors for IgE, FcεRI, are aggregated on the surface of mast cells and basophils. Using a mathematical model of Syk activation the authors investigate two effects, one straightforward and one less so, that result in Syk activation not qualitatively following the cross-linking curve. Model predictions show that if the mechanism by which Syk is fully activated involves the transphosphorylation of Syk by Syk, then Syk activation curves can be either bell shaped or double humped, depending on the cellular concentrations of Syk and FcεRI. The model also predicts that the Syk activation curve can be non-symmetric with respect to the ligand concentration. The cell can exhibit differential Syk activation at two different ligand concentrations that produce identical distributions of receptor aggregates that form and dissociate at the same rates. The authors discuss how, even though it is only receptor aggregates that trigger responses, differences in total ligand concentration can lead to subtle kinetic effects that yield qualitative differences in the levels of Syk activation.Biological mechanisms revealed by a mathematical model for p53–Mdm2 core regulation
http://dl-live.theiet.org/content/journals/10.1049/iet-syb.2008.0152
p53 is a paramount protein in cancer studies, and p53–Mdm2 interaction is the core regulation for most activities of p53 protein-related networks. In this study, a new mathematical model is built to characterise the p53–Mdm2 interaction based on the recent biological findings, as well as a few reasonable hypotheses and approximations. The dynamics of ATM (Ataxia Telangiectasia Mutated) is introduced to the model so as to connect DNA damage signal with the core regulation. The simulation results are in good accord with the experimental observations in the literature. More importantly, through bifurcation analysis on the model, a new threshold mechanism is predicted with respect to the dose of ionising radiation (IR). Furthermore, a novel frequency shifting phenomenon is also observed through Fourier frequency analysis on the simulation data. Finally, based on the predicted dominant frequency, an optimised experimental scheme is proposed to guide the experimental procedure. Once these two predicted mechanisms are validated through wet-lab experiments, they could provide us more insights for p53–Mdm2 core regulation and related pathways.Essay: Defining Systems Biology: An Engineering Perspective
http://dl-live.theiet.org/content/journals/10.1049/iet-syb_20079017
An earlier version of this manuscript appeared in the European Science Foundation Forward Look report on Systems Biology 2007.Oscillations induced by different timescales in signal transduction modules regulated by slowly evolving protein–protein interactions
http://dl-live.theiet.org/content/journals/10.1049/iet-syb.2009.0020
The dynamics induced by the existence of different timescales in a system is explored, in the context of a model composed of activation and signalling modules regulated by a slowly evolving process, such as some particular protein–protein interactions or genetic-like dynamics. It is shown that slowly varying regulation patterns can induce rapid changes in the steady states of the (fast varying) signal transduction pathway, and lead to sustained oscillations. These results are illustrated by a reduced model of the Cdc2–cyclin B cell cycle oscillator. Using available experimental data, parameters of the model are estimated and found to agree with the requirements for a mechanism for oscillatory behaviour arising from coupling fast and slow processes. [Includes supplementary material]Mechanisms of prion disease progression: a chemical reaction network approach
http://dl-live.theiet.org/content/journals/10.1049/iet-syb.2011.0018
Fatal neurodegenerative diseases such as bovine spongiform encephalopathy in cattle, scrapie in sheep and Creutzfeldt–Jakob disease in humans are caused by prions. Prion is a protein encoded by a normal cellular gene. The cellular form of the prion, namely PrP<sup xmlns="http://pub2web.metastore.ingenta.com/ns/"><i>C</i></sup>, is benign but can be converted into a disease-causing form (named scrapie), PrP<sup xmlns="http://pub2web.metastore.ingenta.com/ns/"><i>Sc</i></sup>, by a conformational change from α-helix to β-sheets. Prions replicate by this conformational change; that is, PrP<sup xmlns="http://pub2web.metastore.ingenta.com/ns/"><i>Sc</i></sup> interacts with PrP<sup xmlns="http://pub2web.metastore.ingenta.com/ns/"><i>C</i></sup> producing a new molecule of PrP<sup xmlns="http://pub2web.metastore.ingenta.com/ns/"><i>Sc</i></sup>. This kind of replication is modelled in this contribution as an autocatalytic process. The kinetic model accounts for two of the three epidemiological manifestations: sporadic and infectious. By assuming irreversibility of the PrP<sup xmlns="http://pub2web.metastore.ingenta.com/ns/"><i>Sc</i></sup> replication and describing a first-order reaction for the degradation of cellular tissue, the authors explore dynamical scenarios for prion progression, such as oscillations and conditions for multiplicity of equilibria. Feinberg's chemical reaction network theory is exploited to identify multiple steady states and their associate kinetic constants.Integrating BioPAX pathway knowledge with SBML models
http://dl-live.theiet.org/content/journals/10.1049/iet-syb.2009.0007
Online databases store thousands of molecular interactions and pathways, and numerous modelling software tools provide users with an interface to create and simulate mathematical models of such interactions. However, the two most widespread used standards for storing pathway data (biological pathway exchange; BioPAX) and for exchanging mathematical models of pathways (systems biology markup language; SBML) are structurally and semantically different. Conversion between formats (making data present in one format available in another format) based on simple one-to-one mappings may lead to loss or distortion of data, is difficult to automate, and often impractical and/or erroneous. This seriously limits the integration of knowledge data and models. In this paper we introduce an approach for such integration based on a bridging format that we named systems biology pathway exchange (SBPAX) alluding to SBML and BioPAX. It facilitates conversion between data in different formats by a combination of one-to-one mappings to and from SBPAX and operations within the SBPAX data. The concept of SBPAX is to provide a flexible description expanding around essential pathway data – basically the common subset of all formats describing processes, the substances participating in these processes and their locations. SBPAX can act as a repository for molecular interaction data from a variety of sources in different formats, and the information about their relative relationships, thus providing a platform for converting between formats and documenting assumptions used during conversion, gluing (identifying related elements across different formats) and merging (creating a coherent set of data from multiple sources) data.Conjugation behaviours of CdTe quantum dots and antibody by a novel immunochromatographic method
http://dl-live.theiet.org/content/journals/10.1049/iet-nbt.2010.0001
Three water-soluble CdTe quantum dots (QDs) (green-emitting, yellow-emitting and red-emitting) were synthesised for different refluxing time with 3-mercaptopropionic acid (MPA) as stabiliser. Then the red-emitting CdTe QDs and mouse immunoglobulin G (IgG) were taken as the representative to study the conjugation behaviour of QDs and antibody by a novel immunochromatographic method. After comparing with several methods, that is, direct conjugation, 1-ethyl-3(3-dimethylaminopropyl) carbodiimides hydrochloride (EDC)-mediated conjugation, N-hydroxysuccinimide (NHS)-mediated conjugation, EDC/NHS-mediated conjugation by immunochromatographic strips, EDC and NHS were selected together as coupling agents to conjugate QDs with antibody efficiently. Finally, the K562 leukaemia cells were incubated with the EDC/NHS-mediated conjugates to evaluate the performance in practical application, and the result from fluorescence images showed that it was successfully applied to label cells. The immunochromatographic strip was a superior method to study the conjugation of the fluorophore and antibody.Cross-platform method for identifying candidate network biomarkers for prostate cancer
http://dl-live.theiet.org/content/journals/10.1049/iet-syb.2008.0168
Discovering biomarkers using mass spectrometry (MS) and microarray expression profiles is a promising strategy in molecular diagnosis. Here, the authors proposed a new pipeline for biomarker discovery that integrates disease information for proteins and genes, expression profiles in both genomic and proteomic levels, and protein–protein interactions (PPIs) to discover high confidence network biomarkers. Using this pipeline, a total of 474 molecules (genes and proteins) related to prostate cancer were identified and a prostate-cancer-related network (PCRN) was derived from the integrative information. Thus, a set of candidate network biomarkers were identified from multiple expression profiles composed by eight microarray datasets and one proteomics dataset. The network biomarkers with PPIs can accurately distinguish the prostate patients from the normal ones, which potentially provide more reliable hits of biomarker candidates than conventional biomarker discovery methods.Methods of robustness analysis for Boolean models of gene control networks
http://dl-live.theiet.org/content/journals/10.1049/ip-syb_20050079
As a discrete approach to genetic regulatory networks, Boolean models provide an essential qualitative description of the structure of interactions among genes and proteins. Boolean models generally assume only two possible states (expressed or not expressed) for each gene or protein in the network, as well as a high level of synchronisation among the various regulatory processes. Two possible methods of adapting qualitative models to incorporate the continuous-time character of regulatory networks, are discussed and compared. The first method consists of introducing asynchronous updates in the Boolean model. In the second method, the approach introduced by Glass is adopted to obtain a set of piecewise linear differential equations that continuously describe the states of each gene or protein in the network. Both methods are applied to a Boolean model of the segment polarity gene network of <i xmlns="http://pub2web.metastore.ingenta.com/ns/">Drosophila melanogaster</i>. The dynamics of the model is analysed, and a theoretical characterisation of the model's gene pattern prediction is provided as a function of the timescales of the various processes.Application of graph colouring to biological networks
http://dl-live.theiet.org/content/journals/10.1049/iet-syb.2009.0038
The author explores the application of graph colouring to biological networks, specifically protein–protein interaction (PPI) networks. First, the author finds that given similar conditions (i.e. graph size, degree distribution and clustering), fewer colours are needed to colour disassortative than assortative networks. Fewer colours create fewer independent sets which in turn imply higher concurrency potential for a network. Since PPI networks tend to be disassortative, the author suggests that in addition to functional specificity and stability proposed previously by Maslov and Sneppen (<i xmlns="http://pub2web.metastore.ingenta.com/ns/">Science</i>, <strong xmlns="http://pub2web.metastore.ingenta.com/ns/">296</strong>, 2002), the disassortative nature of PPI networks may promote the ability of cells to perform multiple, crucial and functionally diverse tasks concurrently. Second, because graph colouring is closely related to the presence of cliques in a graph, the significance of node colouring information to the problem of identifying protein complexes (dense subgraphs in PPI networks), is investigated. The author finds that for PPI networks where 1–11% of nodes participate in at least one identified protein complex, such as <i xmlns="http://pub2web.metastore.ingenta.com/ns/">H. sapien</i>, DSATUR (a well-known complete graph colouring algorithm) node colouring information can improve the quality (homogeneity and separation) of initial candidate complexes. This finding may help improve existing protein complex detection methods, and/or suggest new methods. [Includes supplementary material]Domain-oriented reduction of rule-based network models
http://dl-live.theiet.org/content/journals/10.1049/iet-syb_20070081
The coupling of membrane-bound receptors to transcriptional regulators and other effector functions is mediated by multi-domain proteins that form complex assemblies. The modularity of protein interactions lends itself to a rule-based description, in which species and reactions are generated by rules that encode the necessary context for an interaction to occur, but also can produce a combinatorial explosion in the number of chemical species that make up the signalling network. The authors have shown previously that exact network reduction can be achieved using hierarchical control relationships between sites/domains on proteins to dissect multi-domain proteins into sets of non-interacting sites, allowing the replacement of each ‘full’ (progenitor) protein with a set of derived auxiliary (offspring) proteins. The description of a network in terms of auxiliary proteins that have fewer sites than progenitor proteins often greatly reduces network size. The authors describe here a method for automating domain-oriented model reduction and its implementation as a module in the BioNetGen modelling package. It takes as input a standard BioNetGen model and automatically performs the following steps: 1) detecting the hierarchical control relationships between sites; 2) building up the auxiliary proteins; 3) generating a raw reduced model and 4) cleaning up the raw model to provide the correct mass balance for each chemical species in the reduced network. The authors tested the performance of this module on models representing portions of growth factor receptor and immunoreceptor-mediated signalling networks and confirmed its ability to reduce the model size and simulation cost by at least one or two orders of magnitude. Limitations of the current algorithm include the inability to reduce models based on implicit site dependencies or heterodimerisation and loss of accuracy when dynamics are computed stochastically. [Includes supplementary material]Sensitivity analysis predicts that the ERK–pMEK interaction regulates ERK nuclear translocation
http://dl-live.theiet.org/content/journals/10.1049/iet-syb.2009.0010
Following phosphorylation, nuclear translocation of the mitogen-activated protein kinases (MAPKs), ERK1 and ERK2, is critical for both gene expression and DNA replication induced by growth factors. ERK nuclear translocation has therefore been studied extensively, but many details remain unresolved, including whether or not ERK dimerisation is required for translocation. Here, we simulate ERK nuclear translocation with a compartmental computational model that includes systematic sensitivity analysis. The governing ordinary differential equations are solved with the backward differentiation formula and decoupled direct methods. To better understand the regulation of ERK nuclear translocation, we use this model in conjunction with a previously published model of the ERK pathway that does not include an ERK dimer species and with experimental measurements of nuclear translocation of wild-type ERK and a mutant form, ERK1-Δ4, which is unable to dimerise. Sensitivity analysis reveals that the delayed nuclear uptake of ERK1-Δ4 compared to that of wild-type ERK1 can be explained by the altered interaction of ERK1-Δ4 with phosphorylated MEK (MAPK/ERK kinase), and so may be independent of dimerisation. Our study also identifies biological experiments that can verify this explanation.Modelling and analysis of an ensemble of eukaryotic translation initiation models
http://dl-live.theiet.org/content/journals/10.1049/iet-syb.2009.0065
Programmed protein synthesis plays an important role in the cell cycle. Deregulated translation has been observed in several cancers. In this study, the authors constructed an ensemble of mathematical models describing the integration of growth factor signals with translation initiation. Using these models, the authors estimated critical structural features of the translation architecture. Sensitivity and robustness analysis with and without growth factors suggested that a balance between competing regulatory programmes governed translation initiation. Proteins such as Akt and mTor promoted initiation by integrating growth factor signals with the assembly of the 80S initiation complex. However, negative regulators such as PTEN and 4EBP1 restrained initiation in the absence of stimulation. Other proteins such as eIF4E were also found to be structurally critical as deletion of amplification of these components resulted in a network incapable of nominal operation. These findings could help understand the molecular basis of translation deregulation observed in cancer and perhaps lead to new anti-cancer therapeutic strategies. [Includes supplementary material]Control, responses and modularity of cellular regulatory networks: a control analysis perspective
http://dl-live.theiet.org/content/journals/10.1049/iet-syb_20070065
Cells adapt to changes in environmental conditions through the concerted action of signalling, gene expression and metabolic subsystems. The authors will discuss a theoretical framework addressing such integrated systems. This ‘hierarchical analysis’ was first developed as an extension to a metabolic control analysis. It builds on the phenomenon that often the communication between signalling, gene expression and metabolic subsystems is almost exclusively via regulatory interactions and not via mass flow interactions. This allows for the treatment of the said subsystems as ‘levels’ in a hierarchical view of the organisation of the molecular reaction network of cells. Such a hierarchical approach has as a major advantage that levels can be analysed conceptually in isolation of each other (from a local intra-level perspective) and at a later stage integrated via their interactions (from a global inter-level perspective). Hereby, it allows for a modular approach with variable scope. A number of different approaches have been developed for the analysis of hierarchical systems, for example hierarchical control analysis and modular response analysis. The authors, here, review these methods and illustrate the strength of these types of analyses using a core model of a system with gene expression, metabolic and signal transduction levels.