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Steven Johnston

Publications and source records attributed to Steven Johnston.

5 recordsLinked to original sources
PubMed2006

Three hydrolases and a transferase: comparative analysis of active-site dynamics via the BioSimGrid database.

Comparative molecular dynamics (MD) simulations enable us to explore the conformational dynamics of the active sites of distantly related enzymes. We have used the BioSimGrid (http://www.biosimgrid.org) database to facilitate such a comparison. Simulations of four enzymes were analyzed. These included three hydrolases and a transferase, namely acetylcholinesterase, outer-membrane phospholipase A, outer-membrane protease T, and PagP (an outer-membrane enzyme which transfers a palmitate chain from a phospholipid to lipid A). A set of 17 simulations were analyzed corresponding to a total of approximately 0.1 micros simulation time. A simple metric for active-site integrity was used to demonstrate the existence of clusters of dynamic conformational behaviour of the active sites. Small (i.e. within a cluster) fluctuations appear to be related to the function of an enzymatically active site. Larger fluctuations (i.e. between clusters) correlate with transitions between catalytically active and inactive states. Overall, these results demonstrate the potential of a comparative MD approach to analysis of enzyme function. This approach could be extended to a wider range of enzymes using current high throughput MD simulation and database methods.

Acetylcholinesterase↗
PubMed2005

Grid computing and biomolecular simulation.

Biomolecular computer simulations are now widely used not only in an academic setting to understand the fundamental role of molecular dynamics on biological function, but also in the industrial context to assist in drug design. In this paper, two applications of Grid computing to this area will be outlined. The first, involving the coupling of distributed computing resources to dedicated Beowulf clusters, is targeted at simulating protein conformational change using the Replica Exchange methodology. In the second, the rationale and design of a database of biomolecular simulation trajectories is described. Both applications illustrate the increasingly important role modern computational methods are playing in the life sciences.

Biopolymers↗
PubMed2004

BioSimGrid: towards a worldwide repository for biomolecular simulations.

BioSimGrid is a database for biomolecular simulations, or, a "Protein Data Bank extended in time" for molecular dynamics trajectories. We describe the implementation details: architecture, data schema, deposition, and analysis modules. We encourage the simulation community to explore BioSimGrid and work towards a common trajectory exchange format.

Acetylcholinesterase↗
PubMedDate not supplied

Law Enforcement Agency Defibrillation (LEA-D): proceedings of the National Center for Early Defibrillation Police AED Issues Forum.

Why does LEA-D intervention seem to work in some systems but not others? Panelists agreed that some factors that delay rapid access to treatment, such as long travel distances in rural areas, may represent insurmountable barriers. Other factors, however, may be addressed more readily. These include: absence of a medical response culture, discomfort with the role of medical intervention, insecurity with the use of medical devices, a lack of proactive medical direction, infrequent refresher training, and dependence on EMS intervention. Panelists agreed that successful LEA-D programs possess ten key attributes (Table 6). In the end, the goal remains "early" defibrillation, not "police" defibrillation. It does not matter whether the rescuer wears a blue uniform--or any uniform, for that matter--so long as the defibrillator reaches the victim quickly. If LEA personnel routinely arrive at medical emergencies after other emergency responders or after 8 minutes have elapsed from the time of collapse, an LEA-D program will be unlikely to provide added value. Similarly, if police frequently arrive first, but the department is unwilling or unable to cultivate the attributes of successful LEA-D programs, efforts to improve survival may not be realized. In most communities, however, LEA-D programs have tremendous lifesaving potential and are well worth the investment of time and resources. Law enforcement agencies considering adoption of AED programs should review the frequency with which police arrive first at medical emergencies and LEA response intervals to determine whether AED programs might help improve survival in their communities. It is time for law enforcement agency defibrillation to become the rule, not the exception.

Cardiopulmonary Resuscitation↗