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Biomedical subjects

Susan Jones

Publications and source records attributed to Susan Jones.

At least 37 records · Page 2Linked to original sources
PubMed2004

ATP-dependent transcriptional activation by bacterial PspF AAA+protein.

Transcription activation by bacterial sigma(54)-dependent enhancer-binding proteins (EBPs) requires their tri-nucleotide hydrolysis to restructure the sigma(54) RNA polymerase (RNAP). EBPs share sequence similarity with guanine nucleotide binding-proteins and ATPases associated with various cellular activities (AAA) proteins, especially in the mononucleotide binding P-loop fold. Using the phage shock protein F (PspF) EBP, we identify P-loop residues responsible for nucleotide binding and hydrolysis, consistent with their roles in other P-loop NTPases. We show the refined low-resolution structure of an EBP, PspF, revealing a hexameric ring organisation characteristic of AAA proteins. Functioning of EBPs involves ATP binding, higher oligomer formation and ATP hydrolysis coupled to the restructuring of the RNAP. This is thought to be a highly coordinated multi-step process, but the nucleotide-driven mechanism of oligomerisation and ATP hydrolysis is little understood. Our kinetic and structural data strongly suggest that three PspF dimers assemble to form a hexamer upon nucleotide binding. During the ATP hydrolysis cycle, both ATP and ADP are bound to oligomeric PspF, in line with a sequential hydrolysis cycle. We identify a putative R-finger, and show its involvement in ATP hydrolysis. Substitution of this arginine residue results in nucleotide-independent formation of hexameric rings, structurally linking the putative R-finger and, by inference, a specific nucleotide interaction to the control of PspF oligomerisation.

Adenosine Diphosphate↗
PubMed2004

Searching for functional sites in protein structures.

An ability to assign protein function from protein structure is important for structural genomics consortia. The complex relationship between protein fold and function highlights the necessity of looking beyond the global fold of a protein to specific functional sites. Many computational methods have been developed that address this issue. These include evolutionary trace methods, methods that involve the calculation and assessment of maximal superpositions, methods based on graph theory, and methods that apply machine learning techniques. Such function prediction techniques have been applied to the identification of enzyme catalytic triads and DNA-binding motifs.

Binding Sites↗
PubMed2004

Spectral pattern complexity analysis and the quantification of voice normality in healthy and radiotherapy patient groups.

Vocal fold functionality may alter in response to direct radiotherapy or indirectly by perturbation of the hypothalamic-pituitary axis. Perceptual assessment of voice quality is difficult to summarise in a single, reliable figure of normality and normality itself is undefined. In this study spectral analysis of vocal fold vibration, based on impedance variations measured across the larynx using an electro-glottogram, is used to build a single parameter description of standard vowel phonation in the normal male population. Patient data and perceptual assessment are then compared to this standard. The spectral pattern of the vowel/i/ electro-glottogram time series is analysed using approximate entropy after dynamic fundamental-harmonic frequency normalisation. The approximate entropy provides a single estimate of the spectral pattern complexity. A cohort of 89 normal males formed two statistically distinct groups, G1, with strong spectral pattern and high complexity 0.338 (+/-0.036), and G2 with a weak spectral pattern and low complexity 0.175 (+/-0.049). Membership ratio G1:G2 was 2:1. A cohort of 30 male larynx cancer cases were analysed approximately 3-6 months after irradiation, and three male prophylactic cranial irradiation cases some years after treatment. Two-thirds of patients had G2 or lower levels of complexity. The lower G2 complexity level appears to be the subjective, as well as the objective, threshold for voice normality.

Algorithms↗
PubMed2004

Rapid synaptic plasticity of glutamatergic synapses on dopamine neurons in the ventral tegmental area in response to acute amphetamine injection.

Drugs of abuse activate the reward circuitry of the mesocorticolimbic system, and it has been hypothesized that drug exposure triggers synaptic plasticity of glutamatergic synapses onto dopamine (DA) neurons of the ventral tegmental area. Here, we show that just a 2 h in vivo exposure to amphetamine is sufficient to potentiate these synapses, measured as an increase in the synaptic AMPAR/NMDAR ratio. We tested the prediction that an increase in GluR1-containing AMPA receptors would result in an increase in GluR1 homomeric receptors at synapses, but were unable to observe any evidence of the predicted rectification in DA neurons from animals treated with amphetamine. We also examined the possibility of increased AMPA receptor insertion in the membrane, but did not detect a significant increase in biotinylated surface GluR1. We conclude that amphetamine induces rapid changes in synaptic AMPAR/NMDAR ratios, suggesting that potentiation of glutamatergic synapses is a relatively early event in the series of neuroadaptations in response to drugs of abuse.

2-Amino-5-phosphonovalerate↗
PubMed2004

Strengthening the nursing curriculum: an interdisciplinary course addressing agricultural health and safety.

1.) Agricultural work is a dangerous occupation and incorporating content on agricultural health and safety issues into the nursing curriculum presents a challenge. 2.) The traditional strategy for dealing with these issues has been a single discipline approach. 3.) An interdisciplinary course bringing together faculty and students from the disciplines of agriculture, nursing, and public health proved successful in addressing this content in the curricula of the disciplines involved. 4.) When teaching agricultural health and safety content, it is essential to emphasize an interdisciplinary approach and frame the course in the context of rurality.

Agriculture↗
PubMed2003

Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins.

A method to detect DNA-binding sites on the surface of a protein structure is important for functional annotation. This work describes the analysis of residue patches on the surface of DNA-binding proteins and the development of a method of predicting DNA-binding sites using a single feature of these surface patches. Surface patches and the DNA-binding sites were initially analysed for accessibility, electrostatic potential, residue propensity, hydrophobicity and residue conservation. From this, it was observed that the DNA-binding sites were, in general, amongst the top 10% of patches with the largest positive electrostatic scores. This knowledge led to the development of a prediction method in which patches of surface residues were selected such that they excluded residues with negative electrostatic scores. This method was used to make predictions for a data set of 56 non-homologous DNA-binding proteins. Correct predictions made for 68% of the data set.

Binding Sites↗
PubMed2003

A systematic investigation into the effect of protein destabilisation on beta 2-microglobulin amyloid formation.

Beta-2-microglobulin (beta(2)m) has been shown to form amyloid fibrils with distinct morphologies under acidic conditions in vitro. Short, curved fibrils (<600 nm in length), form rapidly without a lag phase, with a maximum rate at pH 3.5. By contrast, fibrils with a long (approximately 1 microm), straight morphology are produced by incubation of the protein at pH< or =3.0. Both fibril types display Congo red birefringence, bind Thioflavin-T and have X-ray fibre diffraction patterns consistent with a cross-beta structure. In order to investigate the role of different partially folded states in generating fibrils of each type, and to probe the effect of protein stability on amyloid formation, we have undertaken a detailed mutagenesis study of beta(2)m. Thirteen variants containing point mutations in different regions of the native protein were created and their structure, stability and fibril forming propensities were investigated as a function of pH. By altering the stability of the native protein in this manner, we show that whilst destabilisation of the native state is important in the generation of amyloid fibrils, population of specific denatured states is a pre-requisite for amyloid formation from this protein. Moreover, we demonstrate that the formation of fibrils with different morphologies in vitro correlates with the relative population of different precursor states.

Amyloid↗
PubMed2003

Role of the N and C-terminal strands of beta 2-microglobulin in amyloid formation at neutral pH.

Beta 2-microglobulin (beta(2)m) is known to form amyloid fibrils de novo in vitro under acidic conditions (below pH 4.8). Fibril formation at neutral pH, however, has only been observed by deletion of the N-terminal six residues; by the addition of pre-assembled seeds; or in the presence of Cu(2+). Based on these observations, and other structural data, models for fibril formation of beta(2)m have been proposed that involve the fraying of the N and C-terminal beta-strands and the consequent loss of edge strand protective features. Here, we examine the role of the N and C-terminal strands in the initiation of fibrillogenesis of beta(2)m by creating point mutations in strands A and G and comparing the properties of the resulting proteins with variants containing similar mutations elsewhere in the protein. We show that truncation of buried hydrophobic side-chains in strands A and G promotes rapid fibril formation at neutral pH, even in unseeded reactions, and increases the rate of fibril formation under acidic conditions. By contrast, similar mutations created in the remaining seven beta-strands of the native protein have little effect on the rate or pH dependence of fibril formation. The data are consistent with the view that perturbation of the N and C-terminal edge strands is an important feature in the generation of assembly-competent states of beta(2)m.

Amyloid↗
PubMed2003

Using structural motif templates to identify proteins with DNA binding function.

This work describes a method for predicting DNA binding function from structure using 3-dimensional templates. Proteins that bind DNA using small contiguous helix-turn-helix (HTH) motifs comprise a significant number of all DNA-binding proteins. A structural template library of seven HTH motifs has been created from non-homologous DNA-binding proteins in the Protein Data Bank. The templates were used to scan complete protein structures using an algorithm that calculated the root mean squared deviation (rmsd) for the optimal superposition of each template on each structure, based on C(alpha) backbone coordinates. Distributions of rmsd values for known HTH-containing proteins (true hits) and non-HTH proteins (false hits) were calculated. A threshold value of 1.6 A rmsd was selected that gave a true hit rate of 88.4% and a false positive rate of 0.7%. The false positive rate was further reduced to 0.5% by introducing an accessible surface area threshold value of 990 A2 per HTH motif. The template library and the validated thresholds were used to make predictions for target proteins from a structural genomics project.

Algorithms↗
PubMed2003

Sequence variation in the CHAT locus shows no association with late-onset Alzheimer's disease.

There is substantial evidence for a susceptibility gene for late-onset Alzheimer's disease (AD) on chromosome 10. One of the characteristic features of AD is the degeneration and dysfunction of the cholinergic system. The genes encoding choline acetyltransferase (ChAT) and its vesicular transporter (VAChT), CHAT and SLC18A3 respectively, map to the linked region of chromosome 10 and are therefore both positional and obvious functional candidate genes for late-onset AD. We have screened both genes for sequence variants and investigated each for association with late-onset AD in up to 500 late-onset AD cases and 500 control DNAs collected in the UK. We detected a total of 17 sequence variants. Of these, 14 were in CHAT, comprising three non-synonymous variants (D7N in the S exon, A120T in exon 5 and L243F in exon 8), one synonymous change (H547H), nine single-nucleotide polymorphisms in intronic, untranslated or promoter regions, and a variable number of tandem repeats in intron 7. Three non-coding SNPs were detected in SLC18A3. None demonstrated any reproducible association with late-onset AD in our samples. Levels of linkage disequilibrium were generally low across the CHAT locus but two of the coding variants, D7N and A120T, proved to be in complete linkage disequilibrium.

Aged↗
PubMed2003

Amyloid-forming peptides from beta2-microglobulin-Insights into the mechanism of fibril formation in vitro.

Beta(2)-Microglobulin (beta(2)m) is one of over 20 proteins known to be involved in human amyloid disease. Peptides equivalent to each of the seven beta-strands of the native protein, together with an eighth peptide (corresponding to the most stable region in the amyloid precursor conformation formed at pH 3.6, that includes residues in the native strand E plus the eight succeeding residues (named peptide E')), were synthesised and their ability to form fibrils investigated. Surprisingly, only two sequences, both of which encompass the region that forms strand E in native beta(2)m, are capable of forming amyloid-like fibrils in vitro. These peptides correspond to residues 59-71 (peptide E) and 59-79 (peptide E') of intact beta(2)m. The peptides form fibrils under the acidic conditions shown previously to promote amyloid formation from the intact protein (pH <5 at low and high ionic strength), and also associate to form fibrils at neutral pH. Fibrils formed from these two peptides enhance fibrillogenesis of the intact protein. No correlation was found between secondary structure propensity, peptide length, pI or hydrophobicity and the ability of the peptides to associate into amyloid-like fibrils. However, the presence of a relatively high content of aromatic side-chains correlates with the ability of the peptides to form amyloid fibrils. On the basis of these results we propose that residues 59-71 may be important in the self-association of partially folded beta(2)m into amyloid fibrils and discuss the relevance of these results for the assembly mechanism of the intact protein in vitro.

Amino Acid Sequence↗
PubMed2003

Preoperative teaching and hysterectomy outcomes.

This study used a theoretical model to determine whether an efficacy-enhancing teaching protocol was effective in improving immediate postoperative behaviors and selected short- and long-term health outcomes in women who underwent abdominal hysterectomies. The model used was the self-efficacy theory of Albert Bandura, PhD. One hundred eight patients in a 486-bed teaching hospital in the Midwest who underwent hysterectomies participated. The participation rate was 85%, and the attrition rate was 17% during the six-month study. The major finding was that participants in the efficacy-enhancing teaching group ambulated significantly longer than participants in the usual care group. This is an important finding because the most prevalent postoperative complications after hysterectomy are atelectasis, pneumonia, paralytic ileus, and deep vein thrombosis, and postoperative ambulation has been shown to decrease or prevent all of these complications. This finding could affect the overall health status of women undergoing hysterectomies.

Adult↗