ORCID Profile
0000-0001-8313-8387
Current Organisations
University of Oxford
,
University of Cambridge
,
University of Melbourne
,
The University of Edinburgh
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Publisher: Elsevier BV
Date: 2004
Publisher: American Chemical Society (ACS)
Date: 20-06-2000
DOI: 10.1021/BI000002W
Abstract: Human apolipoprotein C-II (apoC-II) self-associates in solution to form aggregates with the characteristics of amyloid including red-green birefringence in the presence of Congo Red under cross-polarized light, increased fluorescence in the presence of thioflavin T, and a fibrous structure when examined by electron microscopy. ApoC-II was expressed and purified from Escherichia coli and rapidly exchanged from 5 M guanidine hydrochloride into 100 mM sodium phosphate, pH 7.4, to a final concentration of 0.3 mg/mL. This apoC-II was initially soluble, eluting as low molecular weight species in gel filtration experiments using Sephadex G-50. Circular dichroism (CD) spectroscopy indicated predominantly unordered structure. Upon incubation for 24 h, apoC-II self-associated into high molecular weight aggregates as indicated by elution in the void volume of a Sephadex G-50 column, by rapid sedimentation in an analytical ultracentrifuge, and by increased light scattering. CD spectroscopy indicated an increase in beta-sheet content, while fluorescence emission spectroscopy of the single tryptophan revealed a blue shift and an increase in maximum intensity, suggesting repositioning of the tryptophan into a less polar environment. Electron microscopy of apoC-II aggregates revealed a novel looped-ribbon morphology (width 12 nm) and several isolated closed loops. Like all of the conserved plasma apolipoproteins, apoC-II contains hipathic helical regions that account for the increase in alpha-helix content on lipid binding. The increase in beta-structure accompanying apoC-II fibril formation points to an alternative folding pathway and an in vitro system to explore the general tendency of apolipoproteins to form amyloid in vivo.
Publisher: Springer Science and Business Media LLC
Date: 07-03-2015
Publisher: American Chemical Society (ACS)
Date: 22-08-2006
DOI: 10.1021/JA063751V
Abstract: We have investigated the effect of s le hydration on the wide-angle X-ray scattering patterns of amyloid fibrils from two different sources, hen egg white lysozyme (HEWL) and an 11-residue peptide taken from the sequence of transthyretin (TTR105-115). Both s les show an inter-strand reflection at 4.7 A and an inter-sheet reflection which occurs at 8.8 and approximately 10 A for TTR105-115 and HEWL fibrils, respectively. The positions, widths, and relative intensities of these reflections are conserved in patterns obtained from dried stalks and hydrated s les over a range of fibril concentrations. In 2D scattering patterns obtained from flow-aligned hydrated s les, the inter-strand and inter-sheet reflections showed, respectively, axial and equatorial alignment relative to the fibril axis, characteristic of the cross-beta structure. Our results show that the cross-beta structure of the fibrils is not a product of the dehydrating conditions typically employed to produce aligned s les, but is conserved in in idual fibrils in hydrated s les under dilute conditions comparable to those associated with other biophysical and spectroscopic techniques. This suggests a structure consisting of a stack of two or more sheets whose interfaces are inaccessible to bulk water.
Publisher: Springer Netherlands
Date: 2001
Publisher: American Chemical Society (ACS)
Date: 12-2000
DOI: 10.1021/JA0029580
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C4AN02306D
Abstract: Different mass spectrometry approaches are combined to investigate the conformational flexibility of α-synuclein.
Publisher: Elsevier BV
Date: 08-2011
DOI: 10.1016/J.YMETH.2011.05.004
Abstract: The use of ion mobility mass spectrometry has grown rapidly over the last two decades. This powerful analytical platform now forms an attractive prospect for comprehensive analysis of many different molecular species, including chemically complex biological molecules. This paper describes the application of IM-MS to the study of peptides. We focus on three different ion mobility devices that are most frequently found in tandem with mass spectrometers. These are instruments using linear drift tubes (LDT), those using travelling wave ion guides (TWIGS) and those employing high field asymmetric ion mobility spectrometry (FAIMS). Each technique is described. Ex les are given on the use of IM-MS for the determination of peptide structure, the study of peptides that form amyloid fibrils, and the study of complex peptide mixtures in proteomic investigations. We describe and comment on the methodologies used and the outlook for this developing analytical technique.
Publisher: Elsevier BV
Date: 04-2008
DOI: 10.1016/J.BIOMATERIALS.2007.11.028
Abstract: We describe experiments designed to explore the possibility of using amyloid fibrils as new nanoscale biomaterials for promoting and exploiting cell adhesion, migration and differentiation in vitro. We created peptides that add the biological cell adhesion sequence (RGD) or a control sequence (RAD) to the C-terminus of an 11-residue peptide corresponding to residues 105-115 of the amyloidogenic protein transthyretin. These peptides readily self-assemble in aqueous solution to form amyloid fibrils, and X-ray fibre diffraction shows that they possess the same strand and sheet spacing in the characteristic cross-beta structure as do fibrils formed by the parent peptide. We report that the fibrils containing the RGD sequence are bioactive and that these fibrils interact specifically with cells via the RGD group displayed on the fibril surface. As the design of such functionalized fibrils can be systematically altered, these findings suggest that it will be possible to generate nanomaterials based on amyloid fibrils that are tailored to promote interactions with a wide variety of cell types.
Publisher: Microbiology Society
Date: 13-09-2021
DOI: 10.1099/MIC.0.001082
Abstract: Biofilms are communities of bacteria that are attached to a surface and surrounded by an extracellular matrix. The extracellular matrix protects the community from stressors in the environment, making biofilms robust. The Gram-positive soil bacterium Bacillus subtilis, particularly the isolate NCIB 3610, is widely used as a model for studying biofilm formation. B. subtilis NCIB 3610 forms colony biofilms that are architecturally complex and highly hydrophobic. The hydrophobicity is linked, in part, to the localisation of the protein BslA at the surface of the biofilm, which provides the community with increased resistance to biocides. As most of our knowledge about B. subtilis biofilm formation comes from one isolate, it is unclear if biofilm hydrophobicity is a widely distributed feature of the species. To address this knowledge gap, we collated a library of B. subtilis soil isolates and acquired their whole genome sequences. We used our novel isolates to examine biofilm hydrophobicity and found that, although BslA is encoded and produced by all isolates in our collection, hydrophobicity is not a universal feature of B. subtilis colony biofilms. To test whether the matrix exopolymer poly γ-glutamic acid could be masking hydrophobicity in our hydrophilic isolates, we constructed deletion mutants and found, contrary to our hypothesis, that the presence of poly γ-glutamic acid was not the reason for the observed hydrophilicity. This study highlights the natural variation in the properties of biofilms formed by different isolates and the importance of using a more erse range of isolates as representatives of a species.
Publisher: Elsevier BV
Date: 06-2011
Publisher: Royal Society of Chemistry (RSC)
Date: 2008
DOI: 10.1039/B713013A
Publisher: American Chemical Society (ACS)
Date: 26-01-2006
DOI: 10.1021/JA0565673
Abstract: Protein amyloid fibrils can be functionalized by coating the core protofilament with high concentrations of proteins and enzymes. This can be done elegantly by appending a functional domain to an amyloidogenic protein monomer, then assembling the monomers into a fibril. To display an array of biologically functional porphyrins on the surface of protein fibrils, we have fused the sequence of the small, soluble cytochrome b562 to an SH3 dimer sequence that can form classical amyloid fibrils rapidly under well-defined conditions. The resulting fusion protein also forms amyloid fibrils and, in addition, binds metalloporphyrins, at half of the porphyrin binding sites as shown by UV-vis and NMR spectroscopies. Once metalloporphyrins are bound to the fibrils, the resulting holo-cytochrome domains are spectroscopically identical to the wild type cytochrome. The concentration of metalloporphyrins on a saturated fibril is estimated to be of the order of approximately 20 mM, suggesting that they could be interesting systems for applications in nanotechnology.
Publisher: Royal Society of Chemistry (RSC)
Date: 2009
DOI: 10.1039/B902575H
Publisher: Proceedings of the National Academy of Sciences
Date: 13-04-2015
Abstract: In the natural environment the majority of bacteria live within the confines of a structured social community called a biofilm. The stability of biofilms arises from the extracellular matrix, which consists of proteins, polysaccharides, and extracellular DNA. One of these proteins, BslA, forms a hydrophobic “raincoat” at the surface of the biofilm. We have uncovered the mechanism that enables this protein to function, revealing a structural metamorphosis from a form that is stable in water to a structure that prefers the interface where it self-assembles with nanometer precision to form a robust film. Our findings have wide-ranging implications, from the disruption of harmful bacterial biofilms to the generation of nanoscale materials.
Publisher: Cold Spring Harbor Laboratory
Date: 09-02-2023
DOI: 10.1101/2023.02.09.527868
Abstract: Bacteria engage in competitive interactions with neighbours that can either be of the same or different species. Multiple mechanisms are deployed to ensure the desired outcome and one tactic commonly implemented is the production of specialised metabolites. The Gram-positive bacterium Bacillus subtilis uses specialised metabolites as part of its intraspecies competition determinants to differentiate between kin and non-kin isolates. It is, however, unknown if the collection of specialised metabolites defines competitive fitness when the two isolates start as a close, interwoven community that grows into a densely packed colony biofilm. Moreover, the identity of the most effective specialised metabolites has not been revealed. Here, we determine the competition outcomes that manifest when 21 environmental isolates of B. subtilis are in idually co-incubated with the model isolate NCIB 3610 in a colony biofilm. We correlated these data with the suite of specialised metabolite biosynthesis clusters encoded by each isolate. We found that the epeXEPAB gene cluster correlated with a strong competitive phenotype. This cluster is responsible for producing the epipeptide EpeX. We demonstrated that EpeX is a competition determinant of B. subtilis in an otherwise isogenic context. When we competed the NCIB 3610 EpeX deficient strain against our suite of environmental isolates we found that the impact of EpeX in competition is isolate-specific, as only one of the 21 isolates showed increased survival when EpeX was lacking. Taken together, we have shown that EpeX is a competition determinant used by B. subtilis that impacts intra-species interactions in an isolate-specific manner.
Publisher: Springer Science and Business Media LLC
Date: 05-02-2022
DOI: 10.1038/S41396-022-01198-8
Abstract: Bacteria can form dense communities called biofilms, where cells are embedded in a self-produced extracellular matrix. Exploiting competitive interactions between strains within the biofilm context can have potential applications in biological, medical, and industrial systems. By combining mathematical modelling with experimental assays, we reveal that spatial structure and competitive dynamics within biofilms are significantly affected by the location and density of the founder cells used to inoculate the biofilm. Using a species-independent theoretical framework describing colony biofilm formation, we show that the observed spatial structure and relative strain biomass in a mature biofilm comprising two isogenic strains can be mapped directly to the geographical distributions of founder cells. Moreover, we define a predictor of competitive outcome that accurately forecasts relative abundance of strains based solely on the founder cells’ potential for radial expansion. Consequently, we reveal that variability of competitive outcome in biofilms inoculated at low founder density is a natural consequence of the random positioning of founding cells in the inoculum. Extension of our study to non-isogenic strains that interact through local antagonisms, shows that even for strains with different competition strengths, a race for space remains the dominant mode of competition in low founder density biofilms. Our results, verified by experimental assays using Bacillus subtilis , highlight the importance of spatial dynamics on competitive interactions within biofilms and hence to related applications.
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C4CP05136J
Abstract: Ion mobility mass spectrometry can be combined with data from top-down sequencing to discern adopted conformations of proteins in the absence of solvent.
Publisher: Proceedings of the National Academy of Sciences
Date: 11-07-2017
Abstract: The biofilm matrix is a critical target in the hunt for novel strategies to destabilize or stabilize biofilms. Knowledge of the processes controlling matrix assembly is therefore an essential prerequisite to exploitation. Here, we highlight that the complexity of the biofilm matrix is even higher than anticipated, with one matrix component making two independent functional contributions to the community. The influence the protein exerts is dependent on the local environmental properties, providing another dimension to consider during analysis. These findings add to the evidence that bacteria can evolve multifunctional uses for the extracellular matrix components.
Publisher: Proceedings of the National Academy of Sciences
Date: 20-09-2004
Abstract: Bovine insulin has long been known to self-assemble in vitro into amyloid fibrils. We have observed a further higher-order self-association of the protein into spherical structures, with diameters typically around 50 μm but ranging from 10 to 150 μm. In a polarizing light microscope, these structures exhibit a “Maltese-cross” extinction pattern typical of spherulites. Spherical structures of a similar size distribution can be observed in the environmental scanning electron microscope, which also reveals the presence of significant amounts of water in the structures. The spherulites contain a large quantity of well defined amyloid fibrils, suggesting that they are formed at least in part as a consequence of the self-assembly of preformed fibrils. Similar structures also have been observed in the tissues of patients suffering from amyloid disorders. The ability of amyloid fibrils to form such higher-order assemblies supports the hypothesis that they represent a generic form of polypeptide structure with properties that are analogous to those of classical synthetic polymers.
Publisher: Springer Berlin Heidelberg
Date: 2013
Publisher: Wiley
Date: 23-03-2022
Abstract: An isostructural series of heavy Group 14 E(I) radical anions (Ge, Sn, Pb), stabilized by a bulky xanthene‐based diamido ligand are reported. The radical anions were synthesised by the one‐electron reduction of their corresponding E(II) precursor complexes with sodium naphthalenide in THF, yielding the radical anions as charge‐separated sodium salts. The series of main group radicals have been comprehensively characterized by EPR spectroscopy, X‐ray crystallography and DFT analysis, which reveal that in all cases, the spin density of the unpaired electron almost exclusively resides in a p ‐orbital of π symmetry located on the Group 14 center.
Publisher: Proceedings of the National Academy of Sciences
Date: 19-06-2019
Abstract: Biofilm formation by Bacillus subtilis is a communal process that culminates in the formation of architecturally complex multicellular communities. Here we reveal that the transition of the biofilm into a nonexpanding phase constitutes a distinct step in the process of biofilm development. Using genetic analysis we show that B. subtilis strains lacking the ability to synthesize pulcherriminic acid form biofilms that sustain the expansion phase, thereby linking pulcherriminic acid to growth arrest. However, production of pulcherriminic acid is not sufficient to block expansion of the biofilm. It needs to be secreted into the extracellular environment where it chelates Fe 3+ from the growth medium in a nonenzymatic reaction. Utilizing mathematical modeling and a series of experimental methodologies we show that when the level of freely available iron in the environment drops below a critical threshold, expansion of the biofilm stops. Bioinformatics analysis allows us to identify the genes required for pulcherriminic acid synthesis in other Firmicutes but the patchwork presence both within and across closely related species suggests loss of these genes through multiple independent recombination events. The seemingly counterintuitive self-restriction of growth led us to explore if there were any benefits associated with pulcherriminic acid production. We identified that pulcherriminic acid producers can prevent invasion by neighboring communities through the generation of an “iron-free” zone, thereby addressing the paradox of pulcherriminic acid production by B. subtilis .
Publisher: Wiley
Date: 27-10-1997
DOI: 10.1016/S0014-5793(97)01224-6
Abstract: We have examined the effect of trifluoroethanol (TFE) on the solution behaviour of three hipathic peptides. One of the peptides, containing three heptad repeat units (Ac-YS-(AKEAAKE)3GAR-NH2), remained monomeric under conditions where TFE induced a two-state transition from a random coil to an alpha-helix. In contrast, the TFE-induced alpha-helical formation of two peptides derived from human apolipoproteins C-II and E was accompanied by the formation of discrete dimers and trimers, respectively. The apolipoprotein C-II peptide further aggregated to form beta-sheet at higher concentrations of TFE (50% v/v). The results suggest a class of peptides capable of discrete self-association in the presence of cosolvents which favour intramolecular hydrogen bonding.
Publisher: Proceedings of the National Academy of Sciences
Date: 12-12-2002
Abstract: The molecular conformation of peptide fragment 105–115 of transthyretin, TTR(105–115), previously shown to form amyloid fibrils in vitro , has been determined by magic-angle spinning solid-state NMR spectroscopy. 13 C and 15 N linewidth measurements indicate that TTR(105–115) forms a highly ordered structure with each amino acid in a unique environment. 2D 13 C- 13 C and 15 N- 13 C- 13 C chemical shift correlation experiments, performed on three fibril s les uniformly 13 C, 15 N-labeled in consecutive stretches of 4 aa, allowed the complete sequence-specific backbone and side-chain 13 C and 15 N resonance assignments to be obtained for residues 105–114. Analysis of the 15 N, 13 CO, 13 C α , and 13 C β chemical shifts allowed quantitative predictions to be made for the backbone torsion angles φ and ψ. Furthermore, four backbone 13 C– 15 N distances were determined in two selectively 13 C, 15 N-labeled fibril s les by using rotational-echo double-resonance NMR. The results show that TTR(105–115) adopts an extended β-strand conformation that is similar to that found in the native protein except for substantial differences in the vicinity of the proline residue.
Publisher: Cold Spring Harbor Laboratory
Date: 14-09-2017
DOI: 10.1101/188995
Abstract: Bacterial biofilms are communities of microbial cells encased within a self-produced polymeric matrix. In the Bacillus subtilis biofilm matrix the extracellular fibres of TasA are essential. Here a recombinant expression system allows interrogation of TasA, revealing that monomeric and fibre forms of TasA have identical secondary structure, suggesting that fibrous TasA is a linear assembly of globular units. Recombinant TasA fibres form spontaneously, and share the biological activity of TasA fibres extracted from B. subtilis , whereas a TasA variant restricted to a monomeric form is inactive and subjected to extracellular proteolysis. The biophysical properties of both native and recombinant TasA fibres indicate that they are not functional amyloid-like fibres. A gel formed by TasA fibres can recover after physical shear force, suggesting that the biofilm matrix is not static and that these properties may enable B. subtilis to remodel its local environment in response to external cues. Using recombinant fibres formed by TasA orthologues we uncover species variability in the ability of heterologous fibres to cross-complement the B. subtilis tasA deletion. These findings are indicative of specificity in the biophysical requirements of the TasA fibres across different species and/or reflect the precise molecular interactions needed for biofilm matrix assembly. Conceived and designed the experiments: CE, EE, RG, CEM, RJM, MS, NSW Performed the experiments: KB, LC, CE, EE, PKF, RG, CEM, RJM, MS, TS Contributed new analytical tools: CE, EE, RG, TS Analysed the data: CE, EE, CEM, RJM, MS, LCS, NSW Wrote the paper: EE, RJM, CEM, MS, NSW.
Publisher: Royal Society of Chemistry (RSC)
Date: 2016
DOI: 10.1039/C5CC05801E
Abstract: Transmission electron microscopy and drift tube ion mobility-mass spectrometry are used to study the assemblies formed by the metamorphic chemokine lymphotactin in the presence of a model glycosaminoglycan.
Publisher: Royal Society of Chemistry (RSC)
Date: 2020
DOI: 10.1039/C9SM02141H
Abstract: It is well known that biofilms are one of the most widespread forms of life on Earth, capable of colonising almost any environment from humans to metals.
Publisher: Proceedings of the National Academy of Sciences
Date: 30-10-2023
Publisher: The Royal Society
Date: 28-07-2016
Abstract: Intrinsically interfacially active proteins have garnered considerable interest recently owing to their potential use in a range of materials applications. Notably, the fungal hydrophobins are known to form robust and well-organized surface layers with high mechanical strength. Recently, it was shown that the bacterial biofilm protein BslA also forms highly elastic surface layers at interfaces. Here we describe several self-assembled structures formed by BslA, both at interfaces and in bulk solution, over a range of length scales spanning from nanometres to millimetres. First, we observe transiently stable and highly elongated air bubbles formed in agitated BslA s les. We study their behaviour in a range of solution conditions and hypothesize that their dissipation is a consequence of the slow adsorption kinetics of BslA to an air–water interface. Second, we describe elongated tubules formed by BslA interfacial films when shear stresses are applied in both a Langmuir trough and a rheometer. These structures bear a striking resemblance, although much larger in scale, to the elongated air bubbles formed during agitation. Taken together, this knowledge will better inform the conditions and applications of how BslA can be used in the stabilization of multi-phase materials. This article is part of the themed issue ‘Soft interfacial materials: from fundamentals to formulation’.
Publisher: American Chemical Society (ACS)
Date: 30-07-1999
DOI: 10.1021/BI990726B
Publisher: American Chemical Society (ACS)
Date: 13-08-2009
DOI: 10.1021/JA902825J
Abstract: Small peptides offer an attractive starting point for the development of self-assembling materials for a variety of purposes, since they are relatively simple to produce and can be tailored to provide an expansive range of chemical functionality. We have employed a short peptide that spontaneously self-assembles into a multimolecular fibrillar architecture to drive the coassembly of two independent luminescent moieties. We use fluorescence spectroscopy to demonstrate that the resulting complex performs a light-harvesting function.
Publisher: American Chemical Society (ACS)
Date: 13-08-2010
DOI: 10.1021/BI100864T
Publisher: Cold Spring Harbor Laboratory
Date: 07-10-2019
DOI: 10.1101/794164
Abstract: Biofilm formation is a co-operative behaviour where microbial cells become embedded in an extracellular matrix. This biomolecular matrix plays a key role in the manifestation of the beneficial or detrimental outcome mediated by the collective of cells. Bacillus subtilis is an important bacterium for understanding the general principles of biofilm formation and is a plant growth-promoting organism. The protein components of the B. subtilis matrix include the secreted proteins BslA, which forms a hydrophobic coat over the biofilm, and TasA, which forms protease-resistant fibres needed for structuring. A third protein TapA (for T asA a nchoring and assembly p rotein) is needed for biofilm formation and helps TasA fibre formation in vivo but is dispensable for TasA-fibre assembly in vitro . Here we show that TapA is subjected to proteolytic cleavage in the biofilm and that only the first 57 amino acids of the 253-amino acid protein are required for biofilm architecture. However, through the construction of a strain which lacks all eight extracellular proteases, we show that proteolytic cleavage by these enzymes is not a prerequisite for TapA function. It remains unknown why TapA is synthesized at a full length of 253 amino acids when the first 57 are sufficient for biofilm structuring, but the findings do not exclude the core conserved region of TapA having a second role beyond that of structuring the B. subtilis biofilm.
Publisher: Elsevier BV
Date: 1998
DOI: 10.1016/S0006-3495(98)77804-X
Abstract: In this study, we detected the expression of mRNAs, lncRNAs, and miRNAs in primary cultured leydig cells (LCs) and sertoli cells (SCs) of yak by RNA sequencing technology. A total of 84 differently expression mRNAs (DEmRNAs) (LCs vs. SCs: 15 up and 69 down), 172 differently expression lncRNAs (DElncRNAs) (LCs vs. SCs: 36 up and 136 down), and 90 differently expression miRNAs (DEmiRNAs) (LCs vs. SCs: 72 up and 18 down) were obtained between the two types of cells. GO enrichment and KEGG analysis indicated that the differential expression genes (DEGs) were more enriched in the regulation of actin cytoskeleton, Rap1/MAPK signaling pathway, steroid biosynthesis, focal adhesion, and pathways associated with metabolism. Targeted regulation relationship pairs of 3β-HSD and MSTRG.54630.1, CNTLN and MSTRG.19058.1, BRCA2 and MSTRG.28299.4, CA2 and novel-miR-148, and ceRNA network of LAMC3-MSTRG.68870.1- bta-miR-7862/novel-miR-151/novel-miR-148 were constructed by Cytoscape software. In conclusion, the differences between LCs and SCs were mainly reflected in steroid hormone synthesis, cell proliferation and metabolism, and blood-testicular barrier (BTB) dynamic regulation, and 3β-HSD, CNTLN, BRCA2, CA2, and LAMC3 may be the key factors causing these differences, which may be regulated by ncRNAs. This study provides a basic direction for exploring the differential regulation of LCs and SCs by ncRNAs.
Publisher: Springer Science and Business Media LLC
Date: 17-12-2022
DOI: 10.1038/S41522-022-00361-5
Abstract: A hallmark of microbial biofilms is the self-production of an extracellular molecular matrix that encases the resident cells. The matrix provides protection from the environment, while spatial heterogeneity of gene expression influences the structural morphology and colony spreading dynamics. Bacillus subtilis is a model bacterial system used to uncover the regulatory pathways and key building blocks required for biofilm growth and development. In this work, we report on the emergence of a highly active population of bacteria during the early stages of biofilm formation, facilitated by the extraction of fluid from the underlying agar substrate. We trace the origin of this fluid extraction to the production of poly- γ -glutamic acid (PGA). The flagella-dependent activity develops behind a moving front of fluid that propagates from the boundary of the biofilm towards the interior. The extent of fluid proliferation is controlled by the presence of extracellular polysaccharides (EPS). We also find that PGA production is positively correlated with higher temperatures, resulting in high-temperature mature biofilm morphologies that are distinct from the rugose colony biofilm architecture typically associated with B. subtilis . Although previous reports have suggested that PGA production does not play a major role in biofilm morphology in the undomesticated isolate NCIB 3610, our results suggest that this strain produces distinct biofilm matrices in response to environmental conditions.
Publisher: Cold Spring Harbor Laboratory
Date: 08-07-2021
DOI: 10.1101/2021.07.08.451560
Abstract: Bacteria typically form dense communities called biofilms, where cells are embedded in a self-produced extracellular matrix. Competitive interactions between strains within the biofilm context are studied due to their potential applications in biological, medical, and industrial systems. Combining mathematical modelling with experimental assays, we reveal that the spatial structure and the competitive dynamics within biofilms are significantly affected by the location and density of founder cells. Using an isogenic pair of Bacillus subtilis strains, we show that the observed spatial structure and relative strain biomass in a mature biofilm can be mapped directly to the locations of founder cells. Moreover, we define a predictor of competitive outcome that accurately forecasts relative abundance of strains based solely on the founder cells’ access to free space. Consequently, we reveal that variability of competitive outcome in biofilms inoculated at low founder density is a natural consequence of the random positioning of founding cells in the inoculum. Extending our study to non-isogenic strain pairs of B. subtilis, we show that even for strains with different antagonistic strengths, a race for space remains the dominant mode of competition in biofilms inoculated at low founder densities. Our results highlight the importance of spatial dynamics on competitive interactions within biofilms and hence to related applications.
Publisher: American Chemical Society (ACS)
Date: 28-03-2013
DOI: 10.1021/JZ400372U
Abstract: Amyloid fibrils are self-assembled aggregates of polypeptides that are implicated in the development of several human diseases. A peptide derived from amino acids 105-115 of the human plasma protein transthyretin forms homogeneous and well-defined fibrils and, as a model system, has been the focus of a number of studies investigating the formation and structure of this class of aggregates. Self-assembly of TTR(105-115) occurs at low pH, and this work explores the effect of protonation on the growth and stability of small cross-β aggregates. Using molecular dynamics simulations of structures up to the decamer in both protonated and deprotonated states, we find that, whereas hexamers are more stable for protonated peptides, higher order oligomers are more stable when the peptides are deprotonated. Our findings imply a change in the acid pK of the protonated C-terminal group during the formation of fibrils, which leads to stabilization of higher-order oligomers through electrostatic interactions.
Publisher: Microbiology Society
Date: 08-06-2023
DOI: 10.1099/MIC.0.001344
Abstract: Bacteria engage in competitive interactions with neighbours that can either be of the same or different species. Multiple mechanisms are deployed to ensure the desired outcome and one tactic commonly implemented is the production of specialised metabolites. The Gram-positive bacterium Bacillus subtilis uses specialized metabolites as part of its intra-species competition determinants to differentiate between kin and non-kin isolates. It is, however, unknown if the collection of specialized metabolites defines competitive fitness when the two isolates start as a close, interwoven community that grows into a densely packed colony biofilm. Moreover, the identity of specialized metabolites that have an active role in defining the outcome of an intra-species interaction has not been revealed. Here, we determine the competition outcomes that manifest when 21 environmental isolates of B. subtilis are in idually co-incubated with the model isolate NCIB 3610 in a colony biofilm. We correlated these data with the suite of specialized metabolite biosynthesis clusters encoded by each isolate. We found that the epeXEPAB gene cluster was primarily present in isolates with a strong competitive phenotype. This cluster is responsible for producing the epipeptide EpeX. We demonstrated that EpeX is a competition determinant of B. subtilis in an otherwise isogenic context for NCBI 3610. However, when we competed the NCIB 3610 EpeX-deficient strain against our suite of environmental isolates we found that the impact of EpeX in competition is isolate-specific, as only one of the 21 isolates showed increased survival when EpeX was lacking. Taken together, we have shown that EpeX is a competition determinant used by B. subtilis that impacts intra-species interactions but only in an isolate-specific manner.
Publisher: American Chemical Society (ACS)
Date: 03-2000
DOI: 10.1021/BI992523T
Abstract: Apolipoprotein C-II (apoC-II) is an exchangeable plasma apolipoprotein and an endogenous activator of lipoprotein lipase (LpL). Genetic deficiencies of apoC-II and overexpression of apoC-II in transgenic mice are both associated with severe hyperlipidemia, indicating a complex role for apoC-II in the regulation of blood lipid levels. ApoC-II exerts no effect on the activity of LpL for soluble substrates, suggesting that activation occurs via the formation of a lipid-bound complex. We have synthesized a peptide corresponding to amino acid residues 39-62 of mature human apoC-II. This peptide does not bind to model lipid surfaces but retains the ability to activate LpL. Conjugation of the fluorophore 7-nitrobenz-2-oxa-1,3-diazole (NBD) to the N-terminal alpha-amino group of apoC-II39-62 facilitated determination of the affinity of the peptide for LpL using fluorescence anisotropy measurements. The dissociation constant describing this interaction was 0.23 microM, and was unchanged when LpL was lipid-bound. Competitive binding studies showed that apoC-II39-62 and full-length apoC-II exhibited the same affinity for LpL in aqueous solution, whereas the affinity for full-length apoC-II was increased at least 1 order of magnitude in the presence of lipid. We suggest that while the binding of apoC-II to the lipid surface promotes the formation of a high-affinity complex of apoC-II and LpL, activation occurs via direct helix-helix interactions between apoC-II39-62 and the loop covering the active site of LpL.
Publisher: Springer Berlin Heidelberg
Date: 2013
Publisher: Elsevier BV
Date: 07-2016
Publisher: Wiley
Date: 05-06-2015
Publisher: Proceedings of the National Academy of Sciences
Date: 08-01-2004
Abstract: Amyloid fibrils are self-assembled filamentous structures associated with protein deposition conditions including Alzheimer's disease and the transmissible spongiform encephalopathies. Despite the immense medical importance of amyloid fibrils, no atomic-resolution structures are available for these materials, because the intact fibrils are insoluble and do not form diffraction-quality 3D crystals. Here we report the high-resolution structure of a peptide fragment of the amyloidogenic protein transthyretin, TTR(105–115), in its fibrillar form, determined by magic angle spinning NMR spectroscopy. The structure resolves not only the backbone fold but also the precise conformation of the side chains. Nearly complete 13 C and 15 N resonance assignments for TTR(105–115) formed the basis for the extraction of a set of distance and dihedral angle restraints. A total of 76 self-consistent experimental measurements, including 41 restraints on 19 backbone dihedral angles and 35 13 C– 15 N distances between 3 and 6 Å were obtained from 2D and 3D NMR spectra recorded on three fibril s les uniformly 13 C, 15 N-labeled in consecutive stretches of four amino acids and used to calculate an ensemble of peptide structures. Our results indicate that TTR(105–115) adopts an extended β-strand conformation in the amyloid fibrils such that both the main- and side-chain torsion angles are close to their optimal values. Moreover, the structure of this peptide in the fibrillar form has a degree of long-range order that is generally associated only with crystalline materials. These findings provide an explanation of the unusual stability and characteristic properties of this form of polypeptide assembly.
Publisher: The Royal Society
Date: 16-06-2017
Abstract: Emulsions are a central component of many modern formulations in food, pharmaceuticals, agrichemicals and personal care products. The droplets in these formulations are limited to being spherical as a consequence of the interfacial tension between the dispersed phase and continuous phase. The ability to control emulsion droplet morphology and stabilize non-spherical droplets would enable the modification of emulsion properties such as stability, substrate binding, delivery rate and rheology. One way of controlling droplet microstructure is to apply an elastic film around the droplet to prevent it from relaxing into a sphere. We have previously shown that BslA, an interfacial protein produced by the bacterial genus Bacillus , forms an elastic film when exposed to an oil- or air–water interface. Here, we highlight BslA's ability to stabilize anisotropic emulsion droplets. First, we show that BslA is capable of arresting dynamic emulsification processes leading to emulsions with variable morphologies depending on the conditions and emulsification technique applied. We then show that frozen emulsion droplets can be manipulated to induce partial coalescence. The structure of the partially coalesced droplets is retained after melting, but only when there is sufficient free BslA in the continuous phase. That the fidelity of replication can be tuned by adjusting the amount of free BslA in solution suggests that freezing BslA-stabilized droplets disrupts the BslA film. Finally, we use BslA's ability to preserve emulsion droplet structural integrity throughout the melting process to design emulsion droplets with a chosen shape and size.
Publisher: Cold Spring Harbor Laboratory
Date: 29-04-2021
DOI: 10.1101/2021.04.29.441976
Abstract: Biofilms are communities of bacteria that are attached to a surface and surrounded by an extracellular matrix. The extracellular matrix protects the community from stressors in the environment, making biofilms robust. The Gram-positive soil bacterium Bacillus subtilis , particularly the isolate NCIB 3610, is widely used as a model for studying biofilm formation. B. subtilis NCIB 3610 forms colony biofilms that are architecturally complex and highly hydrophobic. The hydrophobicity is linked, in part, to the localisation of the protein BslA at the surface of the biofilm, which provides the community with increased resistance to biocides. As most of our knowledge about B. subtilis biofilm formation comes from one isolate, it is unclear if biofilm hydrophobicity is a widely distributed feature of the species. To address this knowledge gap, we collated a library of B. subtilis soil isolates and acquired their whole genome sequences. We used our new isolates to examine biofilm hydrophobicity and found that, although BslA is encoded and produced by all isolates in our collection, hydrophobicity is not a universal feature of B. subtilis colony biofilms. To test whether the matrix exopolymer poly γ-glutamic acid could be masking hydrophobicity in our hydrophilic isolates, we constructed deletion mutants and found, contrary to our hypothesis, that the presence of poly γ-glutamic acid was not the reason behind the observed hydrophilicity. This study highlights the natural variation in the properties of biofilms formed by different isolates and the importance of using a more erse range of isolates as representatives of a species. Raw sequence reads and annotated assemblies have been submitted to the European Nucleotide Archive under accession PRJEB43128.
Publisher: Portland Press Ltd.
Date: 11-12-2007
DOI: 10.1042/BJ20060981
Abstract: αB-crystallin is a member of the sHsp (small heat-shock protein) family that prevents misfolded target proteins from aggregating and precipitating. Phosphorylation at three serine residues (Ser19, Ser45 and Ser59) is a major post-translational modification that occurs to αB-crystallin. In the present study, we produced recombi-nant proteins designed to mimic phosphorylation of αB-crystallin by incorporating a negative charge at these sites. We employed these mimics to undertake a mechanistic and structural invest-igation of the effect of phosphorylation on the chaperone activity of αB-crystallin to protect against two types of protein misfolding, i.e. amorphous aggregation and amyloid fibril assembly. We show that mimicking phosphorylation of αB-crystallin results in more efficient chaperone activity against both heat-induced and reduc-tion-induced amorphous aggregation of target proteins. Mimick-ing phosphorylation increased the chaperone activity of αB-crystallin against one amyloid-forming target protein (κ-casein), but decreased it against another (ccβ-Trp peptide). We observed that both target protein identity and solution (buffer) conditions are critical factors in determining the relative chaperone ability of wild-type and phosphorylated αB-crystallins. The present study provides evidence for the regulation of the chaperone activity of αB-crystallin by phosphorylation and indicates that this may play an important role in alleviating the pathogenic effects associated with protein conformational diseases.
Publisher: Proceedings of the National Academy of Sciences
Date: 31-07-2013
Abstract: Biofilms represent the predominant mode of microbial growth in the natural environment. Bacillus subtilis is a ubiquitous Gram-positive soil bacterium that functions as an effective plant growth-promoting agent. The biofilm matrix is composed of an exopolysaccharide and an amyloid fiber-forming protein, TasA, and assembles with the aid of a small secreted protein, BslA. Here we show that natively synthesized and secreted BslA forms surface layers around the biofilm. Biophysical analysis demonstrates that BslA can self-assemble at interfaces, forming an elastic film. Molecular function is revealed from analysis of the crystal structure of BslA, which consists of an Ig-type fold with the addition of an unusual, extremely hydrophobic “cap” region. A combination of in vivo biofilm formation and in vitro biophysical analysis demonstrates that the central hydrophobic residues of the cap are essential to allow a hydrophobic, nonwetting biofilm to form as they control the surface activity of the BslA protein. The hydrophobic cap exhibits physiochemical properties remarkably similar to the hydrophobic surface found in fungal hydrophobins thus, BslA is a structurally defined bacterial hydrophobin. We suggest that biofilms formed by other species of bacteria may have evolved similar mechanisms to provide protection to the resident bacterial community.
Publisher: Wiley
Date: 04-04-2005
Publisher: Springer Science and Business Media LLC
Date: 13-01-2007
DOI: 10.1007/S10856-006-0075-0
Abstract: Synthetic, amyloid-like peptide fibrils have recently attracted interest as a novel, potentially biocompatible material for applications in biotechnology and tissue-engineering. In this paper, we report atomic force microscopy (AFM) studies of the morphology and mechanical stability of fibrils self-assembled in vitro from the short peptide TTR(105-115), which serves as a model system for amyloid fibrils. It forms predominantly straight rods of approximately 1 microm in length and of diameters between 7 nm and 12 nm. We found polymorphism, with some fibrils exhibiting an unstructured morphology and others showing a regular, longitudinal surface pattern of 90 nm periodicity. Contact mode AFM-imaging in air was utilised to perform mechanical tests of in idual fibrils on the nanometer scale with a defined, vertical force in the nN-range applied by the AFM-tip. Above 100 nN, all fibrils showed a permanent, mechanical deformation whereas below 40 nN, fibrils remained unaffected. Tapping-mode AFM-imaging in water led to fibril decomposition within 1.5 h whereas tapping-mode imaging in air left fibrils intact. Additional investigations by circular-dichroism spectroscopy showed that dispersed fibrils were structurally stable in aqueous solution between pH 3 and pH 8, and in sodium phosphate buffer of concentration between 50 mM and 1 M.
Publisher: IOP Publishing
Date: 14-08-2013
DOI: 10.1088/0953-8984/25/37/373101
Abstract: Amyloid and amyloid-like fibrils are self-assembling protein nanostructures, of interest for their robust material properties and inherent biological compatibility as well as their putative role in a number of debilitating mammalian disorders. Understanding fibril formation is essential to the development of strategies to control, manipulate or prevent fibril growth. As such, this area of research has attracted significant attention over the last half century. This review describes a number of different models that have been formulated to describe the kinetics of fibril assembly. We describe the macroscopic implications of mechanisms in which secondary processes such as secondary nucleation, fragmentation or branching dominate the assembly pathway, compared to mechanisms dominated by the influence of primary nucleation. We further describe how experimental data can be analysed with respect to the predictions of kinetic models.
Publisher: Cold Spring Harbor Laboratory
Date: 05-09-2023
Publisher: American Chemical Society (ACS)
Date: 14-10-2015
DOI: 10.1021/ACS.LANGMUIR.5B02347
Abstract: BslA is an hiphilic protein that forms a highly hydrophobic coat around Bacillus subtilis biofilms, shielding the bacterial community from external aqueous solution. It has a unique structure featuring a distinct partition between hydrophilic and hydrophobic surfaces. This surface property is reminiscent of synthesized Janus colloids. By investigating the behavior of BslA variants at water-cyclohexane interfaces through a set of multiscale simulations informed by experimental data, we show that BslA indeed represents a biological ex le of an ellipsoidal Janus nanoparticle, whose surface interactions are, moreover, readily switchable. BslA contains a local conformational toggle, which controls its global affinity for, and orientation at, water-oil interfaces. This adaptability, together with single-point mutations, enables the fine-tuning of its solvent and interfacial interactions, and suggests that BslA could be a basis for biotechnological applications.
Publisher: Springer Science and Business Media LLC
Date: 26-05-2022
DOI: 10.1038/S41522-022-00306-Y
Abstract: The increasing awareness of the significance of microbial biofilms across different sectors is continuously revealing new areas of opportunity in the development of innovative technologies in translational research, which can address their detrimental effects, as well as exploit their benefits. Due to the extent of sectors affected by microbial biofilms, capturing their real financial impact has been difficult. This perspective highlights this impact globally, based on figures identified in a recent in-depth market analysis commissioned by the UK’s National Biofilms Innovation Centre (NBIC). The outputs from this analysis and the workshops organised by NBIC on its research strategic themes have revealed the breath of opportunities for translational research in microbial biofilms. However, there are still many outstanding scientific and technological challenges which must be addressed in order to catalyse these opportunities. This perspective discusses some of these challenges.
Publisher: Springer Berlin Heidelberg
Date: 2013
Publisher: Cold Spring Harbor Laboratory
Date: 21-12-2020
DOI: 10.1101/2020.12.21.423644
Abstract: A hallmark of microbial biofilms is the self-production of extracellular matrix that encases the cells resident within the community. The matrix provides protection from the environment, while spatial heterogeneity of expression influences the structural morphology and colony spreading dynamics. Bacillus subtilis is a model bacterial system used to uncover the regulatory pathways and key building blocks required for biofilm growth and development. Previous reports have suggested that poly- γ -glutamic acid (PGA) production is suppressed during biofilm formation and does not play a major role in biofilm morphology of the undomesticated isolate NCIB 3610. In this work we report on the observation of multiple travelling fronts that develop during the early stage of B. subtilis colony biofilm formation. We find the emergence of a highly motile population of bacteria that is facilitated by the extraction of fluid from the underlying agar substrate. Motility develops behind a moving front of fluid that propagates from the boundary of the biofilm towards the interior. The extent of proliferation is strongly modulated by the presence of extracellular polysaccharides (EPS). We trace the origin of this moving front of fluid to the production of PGA. We find that PGA production is correlated with higher temperatures, resulting in a mature biofilm morphology that is distinct from the biofilm architecture typically associated with B. subtilis . Our results suggest that B. subtilis NCIB 3610 produces distinct biofilm matrices in response to environmental conditions.
Publisher: Proceedings of the National Academy of Sciences
Date: 24-10-2006
Abstract: We report the detailed mechanical characterization of in idual amyloid fibrils by atomic force microscopy and spectroscopy. These self-assembling materials, formed here from the protein insulin, were shown to have a strength of 0.6 ± 0.4 GPa, comparable to that of steel (0.6–1.8 GPa), and a mechanical stiffness, as measured by Young's modulus, of 3.3 ± 0.4 GPa, comparable to that of silk (1–10 GPa). The values of these parameters reveal that the fibrils possess properties that make these structures highly attractive for future technological applications. In addition, analysis of the solution-state growth kinetics indicated a breakage rate constant of 1.7 ± 1.3 × 10 −8 s −1 , which reveals that a fibril 10 μm in length breaks spontaneously on average every 47 min, suggesting that internal fracturing is likely to be of fundamental importance in the proliferation of amyloid fibrils and therefore for understanding the progression of their associated pathogenic disorders.
Publisher: Proceedings of the National Academy of Sciences
Date: 19-03-2013
Abstract: The cross-β amyloid form of peptides and proteins represents an archetypal and widely accessible structure consisting of ordered arrays of β-sheet filaments. These complex aggregates have remarkable chemical and physical properties, and the conversion of normally soluble functional forms of proteins into amyloid structures is linked to many debilitating human diseases, including several common forms of age-related dementia. Despite their importance, however, cross-β amyloid fibrils have proved to be recalcitrant to detailed structural analysis. By combining structural constraints from a series of experimental techniques spanning five orders of magnitude in length scale—including magic angle spinning nuclear magnetic resonance spectroscopy, X-ray fiber diffraction, cryoelectron microscopy, scanning transmission electron microscopy, and atomic force microscopy—we report the atomic-resolution (0.5 Å) structures of three amyloid polymorphs formed by an 11-residue peptide. These structures reveal the details of the packing interactions by which the constituent β-strands are assembled hierarchically into protofilaments, filaments, and mature fibrils.
Publisher: Wiley
Date: 28-10-2010
Publisher: American Chemical Society (ACS)
Date: 06-10-2010
DOI: 10.1021/JP106675H
Publisher: Elsevier BV
Date: 12-2016
DOI: 10.1016/J.MIB.2016.07.012
Abstract: Over the millennia, erse species of bacteria have evolved multiple independent mechanisms to structure sessile biofilm communities that confer protection and stability to the inhabitants. The Gram-positive soil bacterium Bacillus subtilis biofilm presents as an architecturally complex, highly hydrophobic community that resists wetting by water, solvents, and biocides. This remarkable property is conferred by a small secreted protein called BslA, which self-assembles into an organized lattice at an interface. In the biofilm, production of BslA is tightly regulated and the resultant protein is secreted into the extracellular environment where it forms a very effective communal barrier allowing the resident B. subtilis cells to shelter under the protection of a protein raincoat.
Publisher: Elsevier BV
Date: 12-2000
Publisher: Wiley
Date: 15-11-2002
DOI: 10.1093/EMBOJ/CDF609
Abstract: Protein inclusions are associated with a erse group of human diseases ranging from localized neurological disorders through to systemic non-neuropathic diseases. Here, we present evidence that the formation of intranuclear inclusions is a key event in cataract formation involving altered gamma-crystallins that are un likely to adopt their native fold. In three different inherited murine cataracts involving this type of gamma-crystallin mutation, large inclusions containing the altered gamma-crystallins were found in the nuclei of the primary lens fibre cells. Their formation preceded not only the first gross morphological changes in the lens, but also the first signs of cataract. The inclusions contained filamentous material that could be stained with the amyloid-detecting dye, Congo red. In vitro, recombinant mutant gammaB-crystallin readily formed amyloid fibrils under physiological buffer conditions, unlike wild-type protein. These data suggest that this type of cataract is caused by a mechanism involving the nuclear targeting and deposition of amyloid-like inclusions. The mutant gamma-crystallins initially disrupt nuclear function, but then this progresses to a full cataract phenotype.
Publisher: IOP Publishing
Date: 18-12-2015
DOI: 10.1088/1478-3975/12/6/063001
Abstract: Emerging research is revealing a erse array of interfacially-active proteins that are involved in varied biological process from foaming horse sweat to bacterial raincoat formation. We describe an interdisciplinary approach to study the molecular and biophysical mechanisms controlling the activity of an unusual bacterial protein called BslA. This protein is needed for biofilm formation and forms a protective layer or raincoat over the bacterial community, but also has a multitude of potential applications in multiphase formulations. Here we document our journey from fundamental research to an examination of the applications for this surface-active protein in ice cream.
Publisher: IOP Publishing
Date: 05-02-2013
Publisher: American Chemical Society (ACS)
Date: 12-08-2011
DOI: 10.1021/JA203756X
Publisher: Elsevier BV
Date: 04-2005
DOI: 10.1016/J.JMB.2005.01.073
Abstract: A range of disorders such as Alzheimer's disease and type II diabetes have been linked to protein misfolding and aggregation. Transthyretin is an amyloidogenic protein which is involved in familial amyloid polyneuropathy, the most common form of systemic amyloid disease. A peptide fragment of this protein, TTR105-115, has been shown to form well-defined amyloid fibrils in vitro. In this study, the stability of amyloid fibrils towards high hydrostatic pressure has been investigated by Fourier transform infrared spectroscopy. Information on the morphology of the species exposed to high hydrostatic pressure was obtained by atomic force microscopy. The species formed early in the aggregation process were found to be dissociated by relatively low hydrostatic pressure (220 MPa), whereas mature fibrils are pressure insensitive up to 1.3 GPa. The pressure stability of the mature fibrils is consistent with a fibril structure in which there is an extensive hydrogen bond network in a tightly packed environment from which water is excluded. The fact that early aggregates can be dissociated by low pressure suggests, however, that hydrophobic and electrostatic interactions are the dominant factors stabilizing the species formed in the early stages of fibril formation.
Publisher: IEEE
Date: 2006
Publisher: Springer Science and Business Media LLC
Date: 22-11-2016
Publisher: American Chemical Society (ACS)
Date: 12-2005
DOI: 10.1021/BI051352R
Abstract: Caseins are a unique and erse group of proteins present in bovine milk. While their function is presumed to be primarily nutritional, caseins have a remarkable ability to stabilize proteins, i.e., to inhibit protein aggregation and precipitation, that is comparable to molecular chaperones of the small heat-shock protein (sHsp) family. Additionally, sHsps have been shown to inhibit the formation of amyloid fibrils. This study investigated (i) the fibril-forming propensities of casein proteins and their mixture, sodium caseinate, and (ii) the ability of caseins to prevent in vitro fibril formation by kappa-casein. Transmission electron microscopy (TEM) and X-ray fiber diffraction data demonstrated that kappa-casein readily forms amyloid fibrils at 37 degrees C particularly following reduction of its disulfide bonds. The time-dependent increase in thioflavin T fluorescence observed for reduced and nonreduced kappa-casein at 37 degrees C was suppressed by stoichiometric amounts of alphaS- and beta-casein and by the hydrophobic dye 8-anilino-1-naphthalene sulfonate the inhibition of kappa-casein fibril formation under these conditions was verified by TEM. Our findings suggest that alphaS- and beta-casein are potent inhibitors of kappa-casein fibril formation and may prevent large-scale fibril formation in vivo. Casein proteins may therefore play a preventative role in the development of corpora amylacea, a disorder associated with the accumulation of amyloid deposits in mammary tissue.
Publisher: Elsevier BV
Date: 03-2004
Publisher: Cold Spring Harbor Laboratory
Date: 09-03-2019
DOI: 10.1101/570630
Abstract: Biofilm formation by Bacillus subtilis is a communal process that culminates in the formation of architecturally complex multicellular communities. Here we reveal that the transition of the biofilm into a non-expanding phase constitutes a distinct step in the process of biofilm development. Using genetic analysis we show that B. subtilis strains lacking the ability to synthesize pulcherriminic acid form biofilms that sustain the expansion phase, thereby linking pulcherriminic acid to growth arrest. However, production of pulcherriminic acid is not sufficient to block expansion of the biofilm. It needs to be secreted into the extracellular environment where it chelates Fe 3+ from the growth medium in a non-enzymatic reaction. Utilizing mathematical modelling and a series of experimental methodologies we show that when the level of freely available iron in the environment drops below a critical threshold, expansion of the biofilm stops. Bioinformatics analysis allows us to identify the genes required for pulcherriminic acid synthesis in other Firmicutes but the patchwork presence both within and across closely related species suggests loss of these genes through multiple independent recombination events. The seemingly counterintuitive self-restriction of growth led us to explore if there were any benefits associated pulcherriminic acid production. We identified that pulcherriminic acid producers can prevent invasion from neighbouring communities through the generation of an “iron free” zone thereby addressing the paradox of pulcherriminic acid production by B. subtilis . Understanding the processes that underpin the mechanism of biofilm formation, dispersal, and inhibition are critical to allow exploitation and to understand how microbes thrive in the environment. Here, we reveal that the formation of an extracellular iron chelate restricts the expansion of a biofilm. The countering benefit to self-restriction of growth is protection of an environmental niche. These findings highlight the complex options and outcomes that bacteria need to balance in order to modulate their local environment to maximise colonisation, and therefore survival.
Publisher: American Chemical Society (ACS)
Date: 13-12-2013
DOI: 10.1021/JA409050A
Publisher: Wiley
Date: 26-09-2023
DOI: 10.1002/PRO.4736
Abstract: Many proteins that self‐assemble into amyloid and amyloid‐like fibres can adopt erse polymorphic forms. These forms have been observed both in vitro and in vivo and can arise through variations in the steric‐zipper interactions between ꞵ‐sheets, variations in the arrangements between protofilaments, and differences in the number of protofilaments that make up a given fibre class. Different polymorphs arising from the same precursor molecule not only exhibit different levels of toxicity, but importantly can contribute to different disease conditions. However, the factors which contribute to formation of polymorphic forms of amyloid fibrils are not known. In this work, we show that in the presence of 1,2‐dimyristoyl‐sn‐glycero‐3‐phospho‐L‐serine, a highly abundant lipid in the plasma membrane of neurons, the aggregation of α‐synuclein is markedly accelerated and yields a ersity of polymorphic forms under identical experimental conditions. This morphological ersity includes thin and curly fibrils, helical ribbons, twisted ribbons, nanotubes, and flat sheets. Furthermore, the amyloid fibrils formed incorporate lipids into their structures, which corroborates the previous report of the presence of α‐synuclein fibrils with high lipid content in Lewy bodies. Thus, the present study demonstrates that an interface, such as that provided by a lipid membrane, can not only modulate the kinetics of α‐synuclein amyloid aggregation but also plays an important role in the formation of morphological variants by incorporating lipid molecules in the process of amyloid fibril formation. This article is protected by copyright. All rights reserved.
Publisher: American Chemical Society (ACS)
Date: 04-2008
DOI: 10.1021/JA710310C
Abstract: We describe the formation of self-assembling nanoscale fibrillar aggregates from a hybrid system comprising a short polypeptide conjugated to the fluorophore fluorene. The fibrils are typically unbranched, approximately 7 nm in diameter, and many microns in length. A range of techniques are used to demonstrate that the spectroscopic nature of the fluorophore is significantly altered in the fibrillar environment. Time-resolved fluorescence spectroscopy reveals changes in the guest fluorophore, consistent with energy migration and excimer formation within the fibrils. We thus demonstrate the use of self-assembling peptides to drive the assembly of a guest moiety, in which novel characteristics are observed as a consequence. We suggest that this method could be used to drive the assembly of a wide range of guests, offering the development of a variety of useful, smart nanomaterials that are able to self-assemble in a controllable and robust fashion.
Publisher: Cold Spring Harbor Laboratory
Date: 16-06-2022
DOI: 10.1101/2022.06.16.496330
Abstract: Single-species bacterial colony biofilms often present recurring morphologies that are thought to be of benefit to the population of cells within and known to be dependent on the self-produced extracellular matrix. However, much remains unknown in terms of the developmental process at the single cell level. Here, we design and implement systematic time-lapse imaging and quantitative analyses of the growth of Bacillus subtilis colony biofilms. We follow development from the initial deposition of founding cells through to the formation of large-scale complex structures. Using the model biofilm strain NCIB 3610, we examine the movement dynamics of the growing biomass and compare with those displayed by a suite of otherwise isogenic matrix-mutant strains. Correspondingly, we assess the impact of an incomplete matrix on biofilm morphologies and sessile growth rate. Our results indicate that radial expansion of colony biofilms results from ision of bacteria at the biofilm periphery rather than being driven by swelling due to fluid intake. Moreover, we show that lack of exopolysaccharide production has a negative impact on cell ision rate, and the extracellular matrix components act synergistically to give the biomass the structural strength to produce aerial protrusions and agar substrate-deforming ability.
Publisher: Royal Society of Chemistry (RSC)
Date: 2013
DOI: 10.1039/C2AN35665A
Abstract: In the last ten years mass spectrometry has emerged as a powerful biophysical technique capable of providing unique insights into the structure and dynamics of proteins. Part of this explosion in use involves investigations of the most recently 'discovered' subset of proteins: the so-called 'Intrinsically Disordered' or 'Natively Unstructured' proteins. A key advantage of the use of mass spectrometry to study intrinsically disordered proteins (IDPs) is its ability to test biophysical assertions made about why they differ from structured proteins. For ex le, from the charge state distribution presented by a protein following nano-electrospray (n-ESI) it is possible to infer the range of conformations present in solution and hence the extent of disorder n-ESI is highly sensitive to the degree of folding at the moment of transfer from the liquid to the gas phase. The combination of mass spectrometry with ion mobility (IM-MS) provides rotationally averaged collision cross-sections of molecular ions which can be correlated with conformation this too can be applied to IDPs. Another feature which can be monitored by IM-MS is the tendency of disordered proteins to form amyloid fibrils, the protein aggregates involved in the onset of neurodegenerative diseases such as Parkinson's and Alzheimer's. IM-MS provides a useful insight into events that occur during the early stages of aggregation including delineating the structure of the monomer, identifying oligomer distributions, and revealing mechanistic details of the aggregation process. Here we will review the use of MS and IM-MS to study IDPs using ex les from our own and other laboratories.
Publisher: American Chemical Society (ACS)
Date: 29-10-2014
DOI: 10.1021/AC5027435
Abstract: In the past decade, mass spectrometry (MS) coupled with electrospray ionization (ESI) has been extensively applied to the study of intact proteins and their complexes, often without the requirement of labels. Solvent conditions (for ex le, pH, ionic strength, and concentration) affect the observed desolvated species the ease of altering such extrinsic factors renders ESI-MS an appropriate method by which to consider the range of conformational states that proteins may occupy, including natively folded, disordered and amyloid. Rotationally averaged collision cross sections of the ionized forms of proteins, provided by the combination of mass spectrometry and ion mobility (IM-MS), are also instructive in exploring conformational landscapes in the absence of solvent. Here, we ask the following question: "If the only technique you had was ESI-IM-MS, what information would it provide on the structural preferences of an unknown protein?" We have selected 20 different proteins, both monomeric and multimeric, ranging in mass from 2846 Da (melittin) to 150 kDa (Immunoglobulin G), and we consider how they are presented to a mass spectrometer under different solvent conditions. Mass spectrometery allows us to distinguish which of these proteins are structured (melittin, human beta defensin 1, truncated human lymphotactin, Cytochrome C, holo hemoglobin-α, ovalbumin, human transthyretin, avidin, bovine serum albumin, concanavalin, human serum amyloid protein, and Immunoglobulin G) from those that contain at least some regions of disorder (human lymphotactin, N-terminal p53, α-Synuclein, N-terminal MDM2, and p53 DNA binding domain) or denatured due to solvent conditions (ubiquitin, apo hemoglobin-α, apo hemoglobin-β) by considering two experimental parameters: the range of charge states occupied by the protein (Δz) and the range of collision cross sections in which the protein is observed (ΔCCS). We also provide a simple model to predict the difference between the collision cross sections of the most compact and the most extended form of a given protein, based on the volume of the amino acids it contains. We compare these calculated parameters with experimental values. In addition, we consider the occupancy of conformations based on the intensities of ions in the mass spectra. This allows us to qualitatively predict the potential energy landscape of each protein. Our empirical approach to assess order or disorder is shown to be more accurate than the use of charge hydropathy plots, which are frequently used to predict disorder, and could provide an initial route to characterization. Finally, we present an ESI-IM-MS methodology to determine if a given protein is structured or disordered.
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C5AN01253H
Abstract: Mass spectrometry shows insulin oligomers [I] n where n ranges from 1-12, and ion mobility analysis reveals ∼60 structurally distinct species across this oligomer distribution. Experimental data trains MD simulations to characterize a persistent prefibrillar protein oligomer that is a dimer enriched in β sheets.
Publisher: Elsevier BV
Date: 11-1999
Publisher: Elsevier BV
Date: 09-2007
DOI: 10.1016/J.JMB.2007.06.060
Abstract: AlphaB-Crystallin is a ubiquitous small heat-shock protein (sHsp) renowned for its chaperone ability to prevent target protein aggregation. It is stress-inducible and its up-regulation is associated with a number of disorders, including those linked to the deposition of misfolded proteins, such as Alzheimer's and Parkinson's diseases. We have characterised the formation of amyloid fibrils by human alphaB-crystallin in detail, and also that of alphaA-crystallin and the disease-related mutant R120G alphaB-crystallin. We find that the last 12 amino acid residues of the C-terminal region of alphaB-crystallin are predicted from their physico-chemical properties to have a very low propensity to aggregate. (1)H NMR spectroscopy reveals that this hydrophilic C-terminal region is flexible both in its solution state and in amyloid fibrils, where it protrudes from the fibrillar core. We demonstrate, in addition, that the equilibrium between different protofilament assemblies can be manipulated and controlled in vitro to select for particular alphaB-crystallin amyloid morphologies. Overall, this study suggests that there could be a fine balance in vivo between the native functional sHsp state and the formation of amyloid fibrils.
Publisher: Elsevier BV
Date: 04-2000
Publisher: American Chemical Society (ACS)
Date: 20-10-2014
DOI: 10.1021/JP504997K
Abstract: A mass spectrometer provides an ideal laboratory to probe the structure and stability of isolated protein ions. Interrogation of each discrete mass/charge-separated species enables the determination of the intrinsic stability of a protein fold, gaining snapshots of unfolding pathways. In solution, the metamorphic protein lymphotactin (Ltn) exists in equilibrium between two distinct conformations, a monomeric (Ltn10) and a dimeric (Ltn40) fold. Here, we use electron capture dissociation (ECD) and drift tube ion mobility-mass spectrometry (DT IM-MS) to analyze both forms and use molecular dynamics (MD) to consider how the solution fold alters in a solvent-free environment. DT IM-MS reveals significant conformational flexibility for the monomer, while the dimer appears more conformationally restricted. These findings are supported by MD calculations, which reveal how salt bridges stabilize the conformers in vacuo. Following ECD experiments, a distinctive fragmentation pattern is obtained for both the monomer and dimer. Monomer fragmentation becomes more pronounced with increasing charge state especially in the disordered regions and C-terminal α-helix in the solution fold. Lower levels of fragmentation are seen in the β-sheet regions and in regions that contain salt bridges, identified by MD simulations. The lowest charge state of the dimer for which we obtain ECD data ([D+9H](9+)) exhibits extensive fragmentation with no relationship to the solution fold and has a smaller collision cross section (CCS) than charge states 10-13+, suggesting a "collapsed" encounter complex. Other charge states of the dimer, as for the monomer, are resistant to fragmentation in regions of β-sheets in the solution fold. This study provides evidence for preservation and loss of global fold and secondary structural elements, providing a tantalizing glimpse into the power of the emerging field of native top-down mass spectrometry.
Publisher: Elsevier BV
Date: 07-2006
DOI: 10.1016/J.JMB.2006.05.007
Abstract: Amyloid fibrils are typically rigid, unbranched structures with diameters of approximately 10 nm and lengths up to several micrometres, and are associated with more than 20 diseases including Alzheimer's disease and type II diabetes. Insulin is a small, predominantly alpha-helical protein consisting of 51 residues in two disulfide-linked polypeptide chains that readily assembles into amyloid fibrils under conditions of low pH and elevated temperature. We demonstrate here that both the A-chain and the B-chain of insulin are capable of forming amyloid fibrils in isolation under similar conditions, with fibrillar morphologies that differ from those composed of intact insulin. Both the A-chain and B-chain fibrils were found to be able to cross-seed the fibrillization of the parent protein, although these reactions were substantially less efficient than self-seeding with fibrils composed of full-length insulin. In both cases, the cross-seeded fibrils were morphologically distinct from the seeding material, but shared common characteristics with typical insulin fibrils, including a very similar helical repeat. The broader distribution of heights of the cross-seeded fibrils compared to typical insulin fibrils, however, indicates that their underlying protofilament hierarchy may be subtly different. In addition, and remarkably in view of this seeding behavior, the soluble forms of the A-chain and B-chain peptides were found to be capable of inhibiting insulin fibril formation. Studies using mass spectrometry suggest that this behavior might be attributable to complex formation between insulin and the A-chain and B-chain peptides. The finding that the same chemical form of a polypeptide chain in different physical states can either stimulate or inhibit the conversion of a protein into amyloid fibrils sheds new light on the mechanisms underlying fibril formation, fibril strain propagation and amyloid disease initiation and progression.
Publisher: Elsevier BV
Date: 12-2003
Publisher: The Royal Society
Date: 06-05-2003
Abstract: Understanding biological complexity is one of the grand scientific challenges for the future. A living organism is a highly evolved system made up of a large number of interwoven molecular networks. These networks primarily involve proteins, the macromolecules that enable and control virtually every chemical process that takes place in the cell. Proteins are also key elements in the essential characteristic of living systems, their ability to function and replicate themselves through controlled molecular interactions. Recent progress in understanding the most fundamental aspect of polypeptide self-organization, the process by which proteins fold to attain their active conformations, provides a global platform to gain knowledge about the function of biological systems and the regulatory mechanisms that underpin their ability to adapt to changing conditions. In order to exploit such progress effectively, we are developing a variety of approaches, including procedures that use experimental data to restrain the properties of complex systems in computer simulations, to describe their behaviour under a wide variety of conditions. We believe that such approaches can lead to significant advances in understanding biological complexity, in general, and protein folding and misfolding in particular. These advances would contribute to: a more effective exploitation of the information from genome sequences more rational therapeutic approaches to diseases, particularly those associated with ageing the responsible control of our own evolution and the development of new technologies based on mimicking the principles of biological self-assembly, for instance in nanotechnology. More fundamentally, we believe that this research will result in a more coherent understanding of the origin, evolution and functional properties of living systems.
Publisher: Royal Society of Chemistry (RSC)
Date: 2017
DOI: 10.1039/C6CP07261E
Abstract: Using simulation and experiment we investigated the interfacial adsorption of the novel protein surfactant Rsn-2, unveiling the role of its flexible termini in this process.
Publisher: Wiley
Date: 28-10-2010
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Cait MacPhee.