Biomedical subjects

Stephen Wells

Publications and source records attributed to Stephen Wells.

6 recordsLinked to original sources

PubMed2006

The Database of Macromolecular Motions: new features added at the decade mark.

The database of molecular motions, MolMovDB (http://molmovdb.org), has been in existence for the past decade. It classifies macromolecular motions and provides tools to interpolate between two conformations (the Morph Server) and predict possible motions in a single structure. In 2005, we expanded the services offered on MolMovDB. In particular, we further developed the Morph Server to produce improved interpolations between two submitted structures. We added support for multiple chains to the original adiabatic mapping interpolation, allowing the analysis of subunit motions. We also added the option of using FRODA interpolation, which allows for more complex pathways, potentially overcoming steric barriers. We added an interface to a hinge prediction service, which acts on single structures and predicts likely residue points for flexibility. We developed tools to relate such points of flexibility in a structure to particular key residue positions, i.e. active sites or highly conserved positions. Lastly, we began relating our motion classification scheme to function using descriptions from the Gene Ontology Consortium.

Databases, Protein↗

PubMed2005

Constrained geometric simulation of diffusive motion in proteins.

We describe a new computational method, FRODA (framework rigidity optimized dynamic algorithm), for exploring the internal mobility of proteins. The rigid regions in the protein are first determined, and then replaced by ghost templates which are used to guide the movements of the atoms in the protein. Using random moves, the available conformational phase space of a 100 residue protein can be well explored in approximately 10-100 min of computer time using a single processor. All of the covalent, hydrophobic and hydrogen bond constraints are maintained, and van der Waals overlaps are avoided, throughout the simulation. We illustrate the results of a FRODA simulation on barnase, and show that good agreement is obtained with nuclear magnetic resonance experiments. We additionally show how FRODA can be used to find a pathway from one conformation to another. This directed dynamics is illustrated with the protein dihydrofolate reductase.

Algorithms↗

PubMed2004

The influence of transferrin stabilised magnetic nanoparticles on human dermal fibroblasts in culture.

Magnetic nanoparticles have been used for bio-medical purposes including drug delivery, cell destruction and as MRI contrast agents for several years. A more recent biological application has focused on targeted drug delivery. To this end, a wide variety of iron oxide nanoparticles have been synthesised. This study involves the use of magnetic nanoparticles synthesised and derivatised with human transferrin, compared to identical underivatised particles. Human fibroblasts were used, representative of a tissue cell-type. The influence in vitro was determined using light and fluorescence microscopy, scanning and transmission electron microscopy, and 1718 gene microarray. The results indicate that the transferrin derivatised particles appear to localise to the cell membrane without instigating receptor-mediated endocytosis, and also induce up-regulation in the cells for many genes, particularly in the area of cytoskeleton and cell signalling. The microscopy results further support these findings.

Antigens, CD↗

PubMed2004

Cell response to dextran-derivatised iron oxide nanoparticles post internalisation.

Magnetic nanoparticles have been used for many years as magnetic resonance imaging contrast agents. Despite the fact that there are currently several dextran-coated iron oxide nanoparticles are in preclinical and clinical use, there is very little information available concerning the influence such particles have on cells in culture. The prerequisite for particles employed as contrast agents is capture and subsequent uptake by cells. This study involved the use of magnetic nanoparticles synthesised and derivatised with dextran, compared to similar underivatised plain particles. The influence in vitro was assessed using human dermal fibroblasts and various techniques to observe cell-particles interaction, including light and fluorescence microscopy, scanning and transmission electron microscopy. The results indicate that although both the uncoated and the dextran-derivatised particles are uptaken into the cell, the derivatised particles induce alterations in cell behaviour and morphology distinct from the plain particles, suggesting that cell response is dependent on the particles coating.

Adsorption↗

PubMed2004

Surface-modified superparamagnetic nanoparticles for drug delivery: preparation, characterization, and cytotoxicity studies.

Superparamagnetic iron oxide nanoparticles have been used for many years as magnetic resonance imaging (MRI) contrast agents or in drug delivery applications. In this study, a novel approach to prepare magnetic polymeric nanoparticles with magnetic core and polymeric shell using inverse microemulsion polymerization process is reported. Poly(ethyleneglycol) (PEG)-modified superparamagnetic iron oxide nanoparticles with specific shape and size have been prepared inside the aqueous cores of AOT/n-Hexane reverse micelles and characterized by various physicochemical means such as transmission electron microscopy (TEM), infrared spectroscopy, atomic force microscopy (AFM), vibrating sample magnetometry (VSM), and ultraviolet/visible spectroscopy. The inverse microemulsion polymerization of a polymerizable derivative of PEG and a cross-linking agent resulted in a stable hydrophilic polymeric shell of the nanoparticles. The results taken together from TEM and AFM studies showed that the particles are spherical in shape with core-shell structure. The average size of the PEG-modified nanoparticles was found to be around 40-50 nm with narrow size distribution. The magnetic measurement studies revealed the superparamagnetic behavior of the nanoparticles with saturation magnetization values between 45-50 electromagnetic units per gram. The cytotoxicity profile of the nanoparticles on human dermal fibroblasts as measured by standard 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay showed that the particles are nontoxic and may be useful for various in vivo and in vitro biomedical applications.

Cell Survival↗

PubMed2003

Dextran and albumin derivatised iron oxide nanoparticles: influence on fibroblasts in vitro.

Magnetic nanoparticles have been used for biomedical purposes for several years. In recent years, nanotechnology has developed to a stage that makes it possible to engineer particles to provide opportunities for the site-specific delivery of drugs. To this end a variety of iron oxide particles have been synthesised. The size and surface of the particles are crucial factors in the application of the particles. This study therefore involves the use of magnetic nanoparticles synthesised and derivatised with either dextran or albumin, compared to identical underivatised plain particles. This influence in vitro was assessed using human dermal fibroblasts and various techniques to observe cell-particles interaction, including light and fluorescence microscopy, scanning and transmission electron microscopy. The results indicate that the derivatised particles induce alterations in cell behaviour and morphology distinct from the plain particles, suggesting that cell response can be directed via specifically engineered particle surfaces.

Albumins↗