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Biomedical subjects

Mark A Williams

Publications and source records attributed to Mark A Williams.

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

Molecular basis for TPR domain-mediated regulation of protein phosphatase 5.

Protein phosphatase 5 (Ppp5) is a serine/threonine protein phosphatase comprising a regulatory tetratricopeptide repeat (TPR) domain N-terminal to its phosphatase domain. Ppp5 functions in signalling pathways that control cellular responses to stress, glucocorticoids and DNA damage. Its phosphatase activity is suppressed by an autoinhibited conformation maintained by the TPR domain and a C-terminal subdomain. By interacting with the TPR domain, heat shock protein 90 (Hsp90) and fatty acids including arachidonic acid stimulate phosphatase activity. Here, we describe the structure of the autoinhibited state of Ppp5, revealing mechanisms of TPR-mediated phosphatase inhibition and Hsp90- and arachidonic acid-induced stimulation of phosphatase activity. The TPR domain engages with the catalytic channel of the phosphatase domain, restricting access to the catalytic site. This autoinhibited conformation of Ppp5 is stabilised by the C-terminal alphaJ helix that contacts a region of the Hsp90-binding groove on the TPR domain. Hsp90 activates Ppp5 by disrupting TPR-phosphatase domain interactions, permitting substrate access to the constitutively active phosphatase domain, whereas arachidonic acid prompts an alternate conformation of the TPR domain, destabilising the TPR-phosphatase domain interface.

Acyl Coenzyme A↗
PubMed2004

Amygdala responses to fearful and happy facial expressions under conditions of binocular suppression.

The human amygdala plays a crucial role in processing affective information conveyed by sensory stimuli. Facial expressions of fear and anger, which both signal potential threat to an observer, result in significant increases in amygdala activity, even when the faces are unattended or presented briefly and masked. It has been suggested that afferent signals from the retina travel to the amygdala via separate cortical and subcortical pathways, with the subcortical pathway underlying unconscious processing. Here we exploited the phenomenon of binocular rivalry to induce complete suppression of affective face stimuli presented to one eye. Twelve participants viewed brief, rivalrous visual displays in which a fearful, happy, or neutral face was presented to one eye while a house was presented simultaneously to the other. We used functional magnetic resonance imaging to study activation in the amygdala and extrastriate visual areas for consciously perceived versus suppressed face and house stimuli. Activation within the fusiform and parahippocampal gyri increased significantly for perceived versus suppressed faces and houses, respectively. Amygdala activation increased bilaterally in response to fearful versus neutral faces, regardless of whether the face was perceived consciously or suppressed because of binocular rivalry. Amygdala activity also increased significantly for happy versus neutral faces, but only when the face was suppressed. This activation pattern suggests that the amygdala has a limited capacity to differentiate between specific facial expressions when it must rely on information received via a subcortical route. We suggest that this limited capacity reflects a tradeoff between specificity and speed of processing.

Adult↗
PubMed2004

Heat capacity effects of water molecules and ions at a protein-DNA interface.

The interaction of the TATA-box binding protein from the thermophilic and halophilic archaea Pyrococcus woesei (PwTBP) with an oligonucleotide containing a specific binding site is stable over a very broad range of temperatures and ionic strengths, and is consequently an outstanding system for characterising general features of protein-DNA thermodynamics. In common with other specific protein-DNA recognition events, the PwTBP-TATA box interaction is accompanied by a large negative change in heat capacity (deltaCp) arising from the total change in solvation that occurs upon binding, which in this case involves a net uptake of cations. Contrary to previous hypotheses, we find no overall effect of ionic strength on this heat capacity change. We investigate the local contributions of site-specific ion and water binding to the overall change in heat capacity by means of a series of site-directed mutations of PwTBP. We find that although changes in the local ion binding capacity affect the enthalpic and entropic contributions to the free energy of the interaction, they do not affect the change in heat capacity. In contrast, we find remarkably large heat capacity effects arising from two particular symmetry-related mutations. The great magnitude of these effects is not explicable in terms of current semi-empirical models of heat capacity change. Previously reported X-ray crystal structures show that these mutated residues are at the centre of an evolutionarily conserved network of water-mediated hydrogen bonds between the protein and the DNA backbone. Consequently, we conclude that, in addition to water molecules buried in the protein-DNA interface that have been previously shown to influence heat capacity, bridging water molecules in a highly polar surface environment can also contribute substantially to negative heat capacity change on formation of a protein-DNA complex.

Archaeal Proteins↗
PubMed2004

Ulnar artery catheterization with occlusion of corresponding radial artery.

The transradial approach to coronary angiography has become a popular technique. Because of potential advantages, the transulnar approach has also recently been described. We report a successful case of transulnar catheterization with documented occlusion of the radial artery and normal inverse Allen test in a patient with limited vascular access.

Angiography↗
PubMed2004

A unique look at face processing: the impact of masked faces on the processing of facial features.

This experiment utilized a masked priming paradigm to explore the early processes involved in face recognition. The first experiment investigated implicit processing of the eyes and mouth in an upright face, using prime durations of 33 and 50 ms. The results demonstrate implicit processing of both the eyes and mouth, and support the configural processing theory of face processing. The second experiment used the same method with inverted faces and the third experiment was a combination of Experiments 1 and 2. The fourth experiment utilized misaligned faces as the primes. Based on the pattern of results from these experiments, we suggest that, when a face is inverted, the eyes and mouth are initially processed individually and are not linked until a later stage of processing. An upright face is proposed to be processed by analysis of its configuration, whereas an inverted face is initially processed using first-order relational information, and then converted to an upright representation and transferred to face specific regions for configural analysis.

Adult↗
PubMed2004

The extended interface: measuring non-local effects in biomolecular interactions.

Improvements in the sensitivity and availability of biophysical techniques for the detection of the formation of complexes in solution are revealing that the effects of binding are not restricted to the direct contacts between the biomolecules or even to a localised site. Rather, information about the binding event is transmitted throughout the biomolecules and the surrounding solution through changes in the hydrogen bonding, hydration and electrostatic field as the complex is formed. Calorimetric, volumetric and NMR methods are beginning to provide a quantitative view of the nature and thermodynamic consequences of this extended interface, and the resulting data pose a major challenge for computational models of binding.

Biophysical Phenomena↗
PubMed2004

Temporal effects of dialysis on cognitive functioning in patients with ESRD.

BACKGROUND: Although dialysis has been shown to improve cognitive deficits resulting from uremia, little is known about potential temporal variations in cognitive measures between hemodialysis treatments. METHODS: We studied dialysis patients for possible fluctuations in attention and memory by using repeatable neuropsychological measures. Twenty patients undergoing hemodialysis on a thrice-weekly dialysis schedule were assessed at intervals of 1, 24, and 67 hours after the last weekly hemodialysis session. For purposes of comparison, we also studied 10 patients on continuous ambulatory peritoneal dialysis (CAPD) therapy at similar intervals. RESULTS: CAPD patients showed overall stable performance on measures of attention and memory. However, hemodialysis patients showed significant changes (P < 0.05) in auditory memory for both immediate and delayed recall, with the greatest impairment occurring 67 hours postdialysis. Hemodialysis patients also showed a significant change (P < 0.05) in attention between the second and third test periods, ie, 24 to 67 hours postdialysis, with the greatest impairment seen at the 67-hour assessment time. No relationship was found between performance on measures of cognition and levels of postdialysis fatigue in hemodialysis patients. CONCLUSION: CAPD patients showed cognitive stability, whereas hemodialysis patients showed temporal fluctuations in cognitive performance.

Adult↗
PubMed2003

Unconscious perception of non-threatening facial emotion in parietal extinction.

The success of humans as social animals relies heavily on our ability to perceive the emotional expressions conveyed by others' faces. Functional brain imaging has shown that expressions of fear and anger selectively activate the amygdala, even when the faces conveying the emotion are presented briefly and masked to prevent conscious perception (Morris et al. 1998; Whalen et al. 1998). Such results suggest that facial emotions signalling potential threat can be extracted rapidly and automatically by the human visual system, in the absence of conscious face perception. Here we asked whether a patient with spatial extinction, a profound disorder of perception due to right parietal lobe damage, would be sensitive to non-threatening (happy and sad) emotional expressions of faces that are not consciously perceived. We show that the emotion conveyed by an extinguished face in the contralesional hemifield can influence judgements of the emotion of a subsequent target face presented foveally. The finding of significant affective priming from extinguished faces fits with the proposal that facial emotion can be processed in the absence of conscious perception, and that preserved limbic and inferotemporal structures retain privileged access to the emotional content of 'unseen' faces.

Analysis of Variance↗
PubMed2003

Refinement of protein structures in explicit solvent.

We present a CPU efficient protocol for refinement of protein structures in a thin layer of explicit solvent and energy parameters with completely revised dihedral angle terms. Our approach is suitable for protein structures determined by theoretical (e.g., homology modeling or threading) or experimental methods (e.g., NMR). In contrast to other recently proposed refinement protocols, we put a strong emphasis on consistency with widely accepted covalent parameters and computational efficiency. We illustrate the method for NMR structure calculations of three proteins: interleukin-4, ubiquitin, and crambin. We show a comparison of their structure ensembles before and after refinement in water with and without a force field energy term for the dihedral angles; crambin was also refined in DMSO. Our results demonstrate the significant improvement of structure quality by a short refinement in a thin layer of solvent. Further, they show that a dihedral angle energy term in the force field is beneficial for structure calculation and refinement. We discuss the optimal weight for the energy constant for the backbone angle omega and include an extensive discussion of meaning and relevance of the calculated validation criteria, in particular root mean square Z scores for covalent parameters such as bond lengths.

Dimethyl Sulfoxide↗
PubMed2003

NADPH oxidase activation in fibronectin adherent human neutrophils: A potential role for beta1 integrin ligation.

BACKGROUND: Hydrogen peroxide production by human neutrophils is tightly coupled to integrin ligation. This provides a means for spatial localization of oxidant production. However, integrin specificity and consequent signaling mechanisms for this process remain undefined. In the present study we demonstrate that otherwise unstimulated neutrophils adherent to fibronectin, a beta(1) ligand, but not fibrinogen, a beta(2) ligand, produce hydrogen peroxide in a time-dependent fashion. We hypothesized that signaling proceeded through focal, adhesionlike structures. METHODS: Triton-X insoluble (actin cytoskeleton) fractions from suspension phase cells and cells adherent to the beta(1) integrin ligand fibronectin were assessed for the presence of the integrin-associated kinase Pyk2, the scaffolding protein paxillin, and the downstream Src family kinase Lyn. Lysates were subjected to immunoprecipitation with anti-phosphotyrosine and probed for Pyk2, paxillin, and Lyn. Associations between focal adhesion kinase (FAK) and paxillin were determined by immunoprecipitation with anti-FAK and probing with anti-paxillin antibody. Activation of NADPH oxidase was determined by demonstration of redistribution of p47(phox) in Triton-X insoluble fractions. RESULTS: NADPH oxidase activation, as judged by H(2)O(2) production, occurred with fibronectin-, but not in suspension or fibrinogen-adherent cells. Cells adherent to fibronectin for 20 minutes demonstrated marked increases in Pyk2, paxillin, and Lyn activation in comparison to fibronectin-adherent and suspension phase cells. CONCLUSIONS: This study demonstrates that fibronectin adherence is a significant initiating factor for NADPH oxidase assembly in human neutrophils. This appears to be mediated by beta(1) integrins. We demonstrate formation of focal adhesions containing Pyk2/FAK, paxillin, and Lyn, and translocation of p47(phox).

Cell Adhesion↗
PubMed2003

Microbial community dynamics associated with rhizosphere carbon flow.

Root-deposited photosynthate (rhizodeposition) is an important source of readily available carbon (C) for microbes in the vicinity of growing roots. Plant nutrient availability is controlled, to a large extent, by the cycling of this and other organic materials through the soil microbial community. Currently, our understanding of microbial community dynamics associated with rhizodeposition is limited. We used a (13)C pulse-chase labeling procedure to examine the incorporation of rhizodeposition into individual phospholipid fatty acids (PLFAs) in the bulk and rhizosphere soils of greenhouse-grown annual ryegrass (Lolium multiflorum Lam. var. Gulf). Labeling took place during a growth stage in transition between active root growth and rapid shoot growth on one set of plants (labeling period 1) and 9 days later during the rapid shoot growth stage on another set of plants (labeling period 2). Temporal differences in microbial community composition were more apparent than spatial differences, with a greater relative abundance of PLFAs from gram-positive organisms (i15:0 and a15:0) in the second labeling period. Although more abundant, gram-positive organisms appeared to be less actively utilizing rhizodeposited C in labeling period 2 than in labeling period 1. Gram-negative bacteria associated with the 16:1omega5 PLFA were more active in utilizing (13)C-labeled rhizodeposits in the second labeling period than in the first labeling period. In both labeling periods, however, the fungal PLFA 18:2omega6,9 was the most highly labeled. These results demonstrate the effectiveness of using (13)C labeling and PLFA analysis to examine the microbial dynamics associated with rhizosphere C cycling by focusing on the members actively involved.

Carbon↗
PubMed2002

Specificity of chloroplast-localized peptide deformylases as determined with peptide analogs of chloroplast-translated proteins.

Peptide deformylase (DEF; EC 3.5.1.88) removes the N-formyl group from nascent polypeptides. Two nuclear-encoded DEFs in Arabidopsis thaliana (At) are localized to chloroplasts, and thus, the N-termini of chloroplast-translated proteins may be a consequence of AtDEFs' substrate specificity. Using peptide analogs of select chloroplast-translated proteins, AtDEF1 activity was as much as 100-fold lower than AtDEF2 activity and showed little variance with peptide sequence. However, AtDEF2 activity was significantly influenced by peptide sequence, with the most efficiently processed substrate mimicking the N-terminus of the nascent D1 polypeptide, a core protein of photosystem II. Though AtDEF2's specificity was predictive of N-formyl retention for some chloroplast proteins, exceptions suggests that additional factors in vivo aid in determining the retention of an N-formyl group.

Amidohydrolases↗
PubMed2002

Reversal of halophilicity in a protein-DNA interaction by limited mutation strategy.

Comparison of the genes of functionally homologous proteins in organisms existing in different environments shows that adaptation is most often accomplished by mutation of an existing protein. However, from such comparisons, the significance of individual residues to the particular environmental adaptation is not generally discernable among the mass of changes that occur over evolutionary time. This can be exemplified by the general transcription factor found in eukaryotes and archaea, the TATA binding protein (TBP). TBP from Pyrococcus woesei is adapted for optimal binding to DNA at high salt and high temperature, with 34% of the amino acids altered in comparison to its nearest known mesophilic counterpart. We demonstrate that the halophilic nature of this protein can be attributed to only three mutations, revealing that the important phenotype of halophilicity could be rapidly acquired in evolutionary time.

Amino Acid Sequence↗
PubMed2002

Random number generation in autism.

This study explored the ability of individuals with autism to generate a unique series of digits. Fourteen low-functioning individuals with autism, 14 intellectually disabled individuals, and 14 postgraduate university students generated a series of pseudo-random digits. Individuals with autism were more likely to repeat previous digits than were either of the control groups. The normal control group, however, was less likely to attempt cycling through all digits before repeating. Accordingly, low-functioning individuals with autism may exhibit a short-fall in response inhibition. This finding supports the executive dysfunction theory of autism.

Adolescent↗