Biomedical subjects

Stephanie Allen

Publications and source records attributed to Stephanie Allen.

At least 19 recordsLinked to original sources

PubMed2006

Visualizing the solubilization of supported lipid bilayers by an amphiphilic peptide.

The effect of the presequence peptide of cytochrome c oxidase subunit IV (p25) on supported phospholipid bilayers (SPBs) was visualized using atomic force microscopy (AFM). The presequence was found to cause the complete disruption of supported bilayers containing neutral lipids. At relatively low concentrations of presequence, the peptide was found to bind to the membrane, coalescing to form microdomains within the liquid-crystalline bilayer that were located predominantly at bilayer-mica boundaries. Further increases in peptide concentration resulted in the formation of holes within the SPB that were spanned by an interpenetrating network of narrower regions of the bilayer, which, at higher applied peptide concentrations, were observed to disappear through a budding process, ultimately leading to the formation of spherical structures at yet higher peptide concentrations. Within this paper, the impact the presequence has upon the structure and order of the membrane is discussed, as is the potential implication of this apparent solubilization process on the translocation of cytochrome c oxidase into the inner mitochondrial membrane.

Electron Transport Complex IV↗

PubMed2006

Direct observation of the release of phenylalanine from diphenylalanine nanotubes.

The core recognition motif of the amyloidogenic beta-amyloid polypeptide is a dipeptide of phenylalanine. This dipeptide readily self-assembles to form discrete, hollow nanotubes with high persistence lengths. The simplicity of the nanotube formation, combined with ideal physical properties, make these nanotubes highly desirable for a range of applications in bionanotechnology. To fully realize the potential of such structures, it is first necessary to gain a comprehensive understanding of their chemical and physical properties. Previously, the thermal stability of these nanotubes has been investigated by electron microscopy. Here, we further our understanding of the structural stability of the nanotubes upon dry-heating using the atomic force microscope (AFM), and for the first time identify their degradation product utilizing time-of-flight secondary-ion mass spectrometry. We show that the nanotubes are stable at temperatures up to 100 degrees C, but on heating to higher temperatures begin to lose their structural integrity with an apparent collapse in tubular structure. With further increases in temperature up to and above 150 degrees C, there is a degradation of the structure of the nanotubes through the release of phenylalanine building blocks. The breakdown of structure is observed in samples that are either imaged at elevated temperatures or imaged following cooling, suggesting that once phenylalanine is lost from the nanotubes they are susceptible to mechanical deformation by the imaging AFM probe. This temperature-induced plasticity may provide novel properties for these peptide nanotubes, including possible applications as scaffolds and drug delivery devices.

Dipeptides↗

PubMed2006

Thermal and chemical stability of diphenylalanine peptide nanotubes: implications for nanotechnological applications.

The diphenylalanine peptide, the core recognition motif of the beta-amyloid polypeptide, efficiently self-assembles into discrete, well-ordered nanotubes. Here, we describe the notable thermal and chemical stability of these tubular structures both in aqueous solution and under dry conditions. Scanning and transmission electron microscopy (SEM and TEM) as well as atomic force microscopy (AFM) revealed the stability of the nanotubes in aqueous solution at temperatures above the boiling point of water upon autoclave treatment. The nanotubes preserved their secondary structure at temperatures up to 90 degrees C, as shown by circular dichroism (CD) spectra. Cold field emission gun (CFEG) high-resolution scanning electron microscope (HRSEM) and thermogravimetric analysis (TGA) of the peptide nanotubes after dry heat revealed durability at higher temperature. It was shown that the thermal stability of diphenylalanine peptide nanotubes is significantly higher than that of a nonassembling dipeptide, dialanine. In addition to thermal stability, the peptide nanotubes were chemically stable in organic solvents such as ethanol, methanol, 2-propanol, acetone, and acetonitrile, as shown by SEM analysis. Moreover, the acetone environment enabled AFM imaging of the nanotubes in solution. The significant thermal and chemical stability of the peptide nanotubes demonstrated here points toward their possible use in conventional microelectronic and microelectromechanics processes and fabrication into functional nanotechnological devices.

Dipeptides↗

PubMed2006

The DNA-remodelling activity of DnaD is the sum of oligomerization and DNA-binding activities on separate domains.

The Bacillus subtilis DnaD protein is an essential protein that has been implicated in the primosomal step of DNA replication, and recently in global DNA remodelling. Here we show that DnaD consists of two domains with distinct activities; an N-terminal domain (Nd) with oligomerization activity, and a C-terminal domain (Cd) with DNA-binding activity and a second DNA-induced oligomerization activity. Although Cd can bind to DNA and form large nucleoprotein complexes, it does not exhibit global DNA-remodelling activity. The presence of separate Nd does not restore this activity. Our data suggest that the global DNA-remodelling activity of DnaD is the sum of three separate oligomerization and DNA-binding activities residing on two distinct but linked domains.

Amino Acid Motifs↗

PubMed2006

The Bacillus subtilis primosomal protein DnaD untwists supercoiled DNA.

The essential Bacillus subtilis DnaD and DnaB proteins have been implicated in the initiation of DNA replication. Recently, DNA remodeling activities associated with both proteins were discovered that could provide a link between global or local nucleoid remodeling and initiation of replication. DnaD forms scaffolds and opens up supercoiled plasmids without nicking to form open circular complexes, while DnaB acts as a lateral compaction protein. Here we show that DnaD-mediated opening of supercoiled plasmids is accompanied by significant untwisting of DNA. The net result is the conversion of writhe (Wr) into negative twist (Tw), thus maintaining the linking number (Lk) constant. These changes in supercoiling will reduce the considerable energy required to open up closed circular plectonemic DNA and may be significant in the priming of DNA replication. By comparison, DnaB does not affect significantly the supercoiling of plasmids. Binding of the DnaD C-terminal domain (Cd) to DNA is not sufficient to convert Wr into negative Tw, implying that the formation of scaffolds is essential for duplex untwisting. Overall, our data suggest that the topological effects of the two proteins on supercoiled DNA are different; DnaD opens up, untwists and converts plectonemic DNA to a more paranemic form, whereas DnaB does not affect supercoiling significantly and condenses DNA only via its lateral compaction activity. The significance of these findings in the initiation of DNA replication is discussed.

Bacillus subtilis↗

PubMed2005

The Bacillus subtilis DnaD and DnaB proteins exhibit different DNA remodelling activities.

Primosomal protein cascades load the replicative helicase onto DNA. In Bacillus subtilis a putative primosomal cascade involving the DnaD-DnaB-DnaI proteins has been suggested to participate in both the DnaA and PriA-dependent loading of the replicative helicase DnaC onto the DNA. Recently we discovered that DnaD has a global remodelling DNA activity suggesting a more widespread role in bacterial nucleoid architecture. Here, we show that DnaB forms a "square-like" tetramer with a hole in the centre and suggest a model for its interaction with DNA. It has a global DNA remodelling activity that is different from that of DnaD. Whereas DnaD opens up supercoiled DNA, DnaB acts as a lateral compaction protein. The two competing activities can act together on a supercoiled plasmid forming two topologically distinct poles; one compacted with DnaB and the other open with DnaD. We propose that the primary roles of DnaB and DnaD are in bacterial nucleoid architecture control and modulation, and their effects on the initiation of DNA replication are a secondary role resulting from architectural perturbations of chromosomal DNA.

Bacillus subtilis↗

PubMed2005

AFM studies on the role of the protein RdgC in bacterial DNA recombination.

Genetic studies of rdgC in different bacterial systems suggest that it may play a role in replication and recombination. However, the exact function of the corresponding protein, RdgC, is unknown. In this study, we have imaged complexes of RdgC with both linear and supercoiled circular plasmid DNA using atomic force microscopy. We confirm that RdgC does not target any specific sequences in double-stranded DNA, as has been suggested from biochemical data. However, we detect an increased affinity of the protein to DNA ends, and an ability to promote bending of DNA. Similar binding preferences have been reported for enzymes involved in recombination. Protein complexes with supercoiled plasmid DNA further enabled us to study the effect of RdgC on DNA superstructure. At high concentrations of protein we observed promotion of DNA condensation. Recombination is largely enhanced by close contacts of distant regions along the DNA strands, as can occur, for instance, through condensation. Our data thus support a possible function of RdgC as a midwife of recombination.

DNA, Bacterial↗

PubMed2005

Atomic force microscopy study of human amylin (20-29) fibrils.

Here we present atomic force microscopy images of the fibrils formed by human amylin(20-29). This peptide is a fragment of the polypeptide amylin, the major proteinaceous component of amyloid deposits found in cases of type-II diabetes mellitus. Our results demonstrate that the amylin(20-29) peptide fragment forms amyloid-like fibrils that display polymorphic structures. Twisting along the axis of fibrils was often observed in fibrils aged for 6 hours but disappeared in mature fibrils aged for longer time periods.

Amino Acid Sequence↗

PubMed2004

The Bacillus subtilis DnaD protein: a putative link between DNA remodeling and initiation of DNA replication.

The Bacillus subtilis DnaD protein is an essential protein and a component of the oriC and PriA primosomal cascades, which are responsible for loading the main replicative ring helicase DnaC onto DNA. We present evidence that DnaD also has a global DNA architectural activity, assembling into large nucleoprotein complexes on a plasmid and counteracting plasmid compaction in a manner analogous to that recently seen for the histone-like Escherichia coli HU proteins. This DNA-remodeling role may be an essential function for initiation of DNA replication in the Gram +ve B. subtilis, thus highlighting DnaD as the link between bacterial nucleoid reorganization and initiation of DNA replication.

Bacillus subtilis↗

PubMed2004

pH-dependent behavior of surface-immobilized artificial leucine zipper proteins.

The coiled-coil protein motif occurs in over 200 proteins and has generated interest for a range of applications requiring surface immobilization of the constituent peptides. This paper describes an investigation of the environment-responsive behavior of a monolayer of surface-immobilized artificial proteins, which are known to assemble to form coiled-coil structures in bulk solution. An extended version of the quartz crystal microbalance (QCM-D) and surface plasmon resonance (SPR) are independently employed to characterize the adsorption of the proteins to a gold surface. The data suggest that the molecules arrange in a closely packed layer orientated perpendicular to the surface. QCM-D measurements are also employed to measure pH-induced changes in the resonant frequency (f) and the energy dissipation factor (D) of a gold-coated quartz crystal functionalized with the formed monolayer. Exposure of the protein monolayer to a pH 4.5 solution results in a shift of 43 Hz in f and a shift of -0.7 x 10(-6) in D as compared to pH 7.4. In contrast, increasing the pH to 11.2, results in f and D shifts of -17 Hz and 0.6 x 10(-6), respectively. The magnitude of the observed shifts suggests that the proteins form a rigid layer at low pH that can be hydrated to a fluid layer as the pH is increased. These observations correlate with spectroscopic changes that indicate a reduction in the helical content of the protein in bulk solutions of high pH.

Adsorption↗

PubMed2004

DnaG interacts with a linker region that joins the N- and C-domains of DnaB and induces the formation of 3-fold symmetric rings.

Loading of the replicative ring helicase onto the origin of replication (oriC) is the final outcome of a well coordinated series of events that collectively constitute a primosomal cascade. Once the ring helicase is loaded, it recruits the primase and signals the switch to the polymerization mode. The transient nature of the helicase-primase (DnaB-DnaG) interaction in the Escherichia coli system has hindered our efforts to elucidate its structure and function. Taking advantage of the stable DnaB-DnaG complex in Bacillus stearothermophilus, we have reviewed conflicting mutagenic data from other bacterial systems and shown that DnaG interacts with the flexible linker that connects the N- and C-terminal domains of DnaB. Furthermore, atomic force microscopy (AFM) imaging experiments show that binding of the primase to the helicase induces predominantly a 3-fold symmetric morphology to the hexameric ring. Overall, three DnaG molecules appear to interact with the hexameric ring helicase but a small number of complexes with two and even one DnaG molecule bound to DnaB were also detected. The structural/functional significance of these data is discussed and a speculative structural model for this complex is suggested.

Bacterial Proteins↗

PubMed2004

The clamp-loader-helicase interaction in Bacillus. Atomic force microscopy reveals the structural organisation of the DnaB-tau complex in Bacillus.

The clamp-loader-helicase interaction is an important feature of the replisome. Although significant biochemical and structural work has been carried out on the clamp-loader-clamp-DNA polymerase alpha interactions in Escherichia coli, the clamp-loader-helicase interaction is poorly understood by comparison. The tau subunit of the clamp-loader mediates the interaction with DnaB. We have recently characterised this interaction in the Bacillus system and established a tau(5)-DnaB(6) stoichiometry. Here, we have obtained atomic force microscopy images of the tau-DnaB complex that reveal the first structural insight into its architecture. We show that despite the reported absence of the shorter gamma version in Bacillus, tau has a domain organisation similar to its E.coli counterpart and possesses an equivalent C-terminal domain that interacts with DnaB. The interaction interface of DnaB is also localised in its C-terminal domain. The combined data contribute towards our understanding of the bacterial replisome.

Adenosine Triphosphatases↗

PubMed2004

Influence of architecture on the kinetic stability of molecular assemblies.

The strength of a multimolecular system depends on the number of interactions that hold it together. Using dynamic force spectroscopy, we show how the kinetic stability of a system decreases as the number of molecular bonds is increased, as predicted by theory. The data raise important considerations for experimental tests of bond strength and, as a paradigm, suggest both routes to and pitfalls in methods for computational simulation of molecular transitions, such as ligand binding and protein folding.

Biotin↗

PubMed2004

An atomic force microscopy study of the effect of nanoscale contact geometry and surface chemistry on the adhesion of pharmaceutical particles.

PURPOSE: To understand differences in particle adhesion observed with increasing humidity between samples of salbutamol sulfate prepared by two different methods. METHODS: Atomic force microscopy (AFM) force measurements were performed as a function of humidity (<10% to 65% RH) using two systems. The first system used clean AFM tips against compressed disks of micronized and solution enhanced dispersion by supercritical fluid (SEDS) salbutamol. The second system involved particles of both salbutamol samples mounted onto the apexes of AFM cantilevers, and force measurements being performed against a highly orientated pyrolytic graphite (HOPG) substrate. Following these measurements, the contact asperities of the tips were characterized. RESULTS: The first system showed a maximum in the observed adhesion at 22% relative humidity (RH) for the SEDS salbutamol compared to 44% RH for the micronized salbutamol. The second system showed a mix of peaks and continual increases in adhesion with humidity. The predicted Johnson-Kendall-Roberts forces were calculated and divided by the actual forces in order to produce a ratio. CONCLUSIONS: By relating the nature of the asperities to the force measurements, we propose a model in which adhesion scenarios range from single asperity nanometer-scale contact in which peaks in the adhesion were observed, to multiasperity contact where a continuous increase in adhesion was seen with humidity.

Adhesiveness↗

PubMed2004

Evaluation of the kinetic properties of the sporulation protein SpoIIE of Bacillus subtilis by inclusion in a model membrane.

Starvation induces Bacillus subtilis to initiate a developmental process (sporulation) that includes asymmetric cell division to form the prespore and the mother cell. The integral membrane protein SpoIIE is essential for the prespore-specific activation of the transcription factor sigmaF, and it also has a morphogenic activity required for asymmetric division. An increase in the local concentration of SpoIIE at the polar septum of B. subtilis precedes dephosphorylation of the anti-anti-sigma factor SpoIIAA in the prespore. After closure and invagination of the asymmetric septum, phosphatase activity of SpoIIE increases severalfold, but the reason for this dramatic change in activity has not been determined. The central domain of SpoIIE has been seen to self-associate (I. Lucet et al., EMBO J. 19:1467-1475, 2000), suggesting that activation of the C-terminal PP2C-like phosphatase domain might be due to conformational changes brought about by the increased local concentration of SpoIIE in the sporulating septum. Here we report the inclusion of purified SpoIIE protein into a model membrane as a method for studying the effect of local concentration in a lipid bilayer on activity. In vitro assays indicate that the membrane-bound enzyme maintains dephosphorylation rates similar to the highly active micellar state at all molar ratios of protein to lipid. Atomic force microscopy images indicate that increased local concentration does not lead to self-association.

Bacillus subtilis↗

PubMed2004

Single-molecule investigations of RNA dissociation.

Given the essential cellular roles for ribonucleic acids (RNAs) it is important to understand the stability of three-dimensional structures formed by these molecules. This study aims to investigate the dissociation energy landscape for simple RNA structures via atomic-force-microscopy-based single-molecule force-spectroscopy measurements. This approach provides details on the locations and relative heights of the energy barriers to dissociation, and thus information upon the relative kinetic stabilities of the formed complexes. Our results indicate that a simple dodecamer RNA helix undergoes a forced dissociation process similar to that previously observed for DNA oligonucleotides. Incorporating a UCU bulge motif is found to introduce an additional energy barrier closer to the bound state, and also to destabilize the duplex. In the absence of magnesium ions a duplex containing this UCU bulge is destabilized and a single, shorter duplex is formed. These results reveal that a bulge motif impacts upon the forced dissociation of RNA and produces an energy landscape sensitive to the presence of magnesium ions. Interestingly, the obtained data compare well with previously reported ensemble measurements, illustrating the potential of this approach to improve our understanding of RNA stability and dissociation kinetics.

Magnesium↗

PubMed2003

Direct real-time molecular scale visualisation of the degradation of condensed DNA complexes exposed to DNase I.

The need to protect DNA from in vivo degradation is one of the basic tenets of therapeutic gene delivery and a standard test for any proposed delivery vector. The currently employed in vitro tests, however, presently provide no direct link between the molecular structure of the vector complexes and their success in this role, thus hindering the rational design of successful gene delivery agents. Here we apply atomic force microscopy (AFM) in liquid to visualise at the molecular scale and in real time, the effect of DNase I on generation 4 polyamidoamine dendrimers (G4) complexed with DNA. These complexes are revealed to be dynamic in nature showing a degree of mobility, in some cases revealing the addition and loss of dendrimers to individual complexes. The formation of the G4-DNA complexes is observed to provide a degree of protection to the DNA. This protection is related to the structural morphology of the formed complex, which is itself shown to be dependent on the dendrimer loading and the time allowed for complex formation.

DNA↗

PubMed2003

Characterization of particle-interactions by atomic force microscopy: effect of contact area.

PURPOSE: The purpose of this work was to compare adhesion forces, contact area, and work of adhesion of salbutamol sulphate particles produced using micronization and a supercritical fluid technique (solution-enhanced dispersion by supercritical fluids--SEDS) using atomic force microscopy (AFM). METHODS: Adhesion forces of individual particles of micronized and SEDS salbutamol against a highly orientated pyrolytic graphite surface were acquired in a liquid environment consistent with that of a pressurized metered dose inhaler. The forces were then related to contact area and work of adhesion. RESULTS: The raw adhesion force data for the micronized and SEDS material were 14.1 nN (SD 2.5 nN) and 4.2 nN (SD 0.8 nN), respectively. After correction for contact area, the forces per unit area were 13 mN/microm2 (SD 2.3 mN/microm2) and 3 mN/microm2 (SD 0.6 mN/microm2). The average work of adhesion was calculated using the Johnson-Kendall-Roberts theory and was found to be 19 mJm(-2) (SD 3.4 mJm(-2)) for the micronized particle and 4 mJm(-2) (SD 0.8 mJm(-2)) for the SEDS particle. CONCLUSIONS: It is possible to produce a three-dimensional representation of the contact area involved in the interaction and make quantitative comparisons between different particles. There was a lower force per unit area and work of adhesion observed for the SEDS material, possibly because of its lower surface free energy.

Albuterol↗