PubMed Health⌕ Search

Biomedical subjects

Heather L Gordon

Publications and source records attributed to Heather L Gordon.

6 recordsLinked to original sources
PubMed2006

Local-structural diversity and protein folding: application to all-beta off-lattice protein models.

Global measures of structural diversity within a distribution of biopolymers, such as the radius of gyration and percent native contacts, have proven useful in the analysis of simulation data for protein folding. In this paper we describe a statistical-based methodology to quantify the local structural variability of a distribution of biopolymers, applied to 46- and 69-"residue" off-lattice, three-color model proteins. Each folds into beta-barrel structures. First we perform a principal component analysis of all interbead distance variables for a large number of independent, converged Boltzmann-distributed samples of conformations collected at each of a wide range of temperatures. Next, the principal component vectors are subjected to orthogonal (varimax) rotation. The results are displayed on so-called "squared-loading" plots. These provide a quantitative measure of the contribution to the sample variance of the position of each residue relative to the others. Dominant structural elements, those having the largest structural diversity within the sampled distribution, are responsible for peaks and shoulders observed in the specific heat versus temperature curves, generated using the weighted histogram analysis method. The loading plots indicate that the local-structural diversity of these systems changes gradually with temperature through the folding transition but radically changes near the collapse transition temperature. The analysis of the structural overlap order statistic suggests that the 46-mer thermodynamic folding transition involves the native state and at least three other nearly native intermediates. In the case of the 46-mer protein model, data are generated at sufficiently low temperatures that squared-loading plots, coupled with cluster analysis, provide a local and energetic description of its glassy state.

Algorithms↗
PubMed2005

Functionally relevant protein motions: extracting basin-specific collective coordinates from molecular dynamics trajectories.

Functionally relevant motion of proteins has been associated with a number of atoms moving in a concerted fashion along so-called "collective coordinates." We present an approach to extract collective coordinates from conformations obtained from molecular dynamics simulations. The power of this technique for differentiating local structural fluctuations between classes of conformers obtained by clustering is illustrated by analyzing nanosecond-long trajectories for the response regulator protein Spo0F of Bacillus subtilis, generated both in vacuo and using an implicit-solvent representation. Conformational clustering is performed using automated histogram filtering of the inter-C(alpha) distances. Orthogonal (varimax) rotation of the vectors obtained by principal component analysis of these interresidue distances for the members of individual clusters is key to the interpretation of collective coordinates dominating each conformational class. The rotated loadings plots isolate significant variation in interresidue distances, and these are associated with entire mobile secondary structure elements. From this we infer concerted motions of these structural elements. For the Spo0F simulations employing an implicit-solvent representation, collective coordinates obtained in this fashion are consistent with the location of the protein's known active sites and experimentally determined mobile regions.

Amino Acid Sequence↗
PubMed2004

Functional differences among those high and low on a trait measure of psychopathy.

BACKGROUND: It has been established that individuals who score high on measures of psychopathy demonstrate difficulty when performing tasks requiring the interpretation of other's emotional states. The aim of this study was to elucidate the relation of emotion and cognition to individual differences on a standard psychopathy personality inventory (PPI) among a nonpsychiatric population. METHODS: Twenty participants completed the PPI. Following survey completion, a mean split of their scores on the emotional-interpersonal factor was performed, and participants were placed into a high or low group. Functional magnetic resonance imaging data were collected while participants performed a recognition task that required attention be given to either the affect or identity of target stimuli. RESULTS: No significant behavioral differences were found. In response to the affect recognition task, significant differences between high- and low-scoring subjects were observed in several subregions of the frontal cortex, as well as the amygdala. No significant differences were found between the groups in response to the identity recognition condition. CONCLUSIONS: Results indicate that participants scoring high on the PPI, although not behaviorally distinct, demonstrate a significantly different pattern of neural activity (as measured by blood oxygen level-dependent contrast)in response to tasks that require affective processing. The results suggest a unique neural signature associated with personality differences in a nonpsychiatric population.

Adult↗
PubMed2003

An fMRI investigation of the impact of interracial contact on executive function.

We investigated whether individual differences in racial bias among white participants predict the recruitment, and potential depletion, of executive attentional resources during contact with black individuals. White individuals completed an unobtrusive measure of racial bias, then interacted with a black individual, and finally completed an ostensibly unrelated Stroop color-naming test. In a separate functional magnetic resonance imaging (fMRI) session, subjects were presented with unfamiliar black male faces, and the activity of brain regions thought to be critical to executive control was assessed. We found that racial bias predicted activity in right dorsolateral prefrontal cortex (DLPFC) in response to black faces. Furthermore, activity in this region predicted Stroop interference after an actual interracial interaction, and it statistically mediated the relation between racial bias and Stroop interference. These results are consistent with a resource depletion account of the temporary executive dysfunction seen in racially biased individuals after interracial contact.

Adult↗
PubMed2003

Neural correlates of thought suppression.

The present report used functional magnetic resonance imaging (fMRI) to examine the neural correlates of thought suppression. Subjects were imaged while alternately (i) attempting to suppress a particular thought, (ii) attempting to suppress all thoughts, or (iii) thinking freely about any thought. Suppression of a particular thought, when compared to the free-thought control condition, revealed greater activation in the anterior cingulate. When the task of suppressing all conscious thoughts was compared to free-thought, a more distributed network of brain regions, including the anterior cingulate and the insula, was activated. These findings are consistent with previous research on cognitive control and may provide potential insights into psychological disorders involving recurring, intrusive thoughts.

Adult↗