0000000000122211
AUTHOR
Daniel J. White
Nanoscale Engineering in the Biosciences
Biological matter is one of the most diverse and important classes of materials. Products of living organisms (wood, bone, cotton, wool, leather, coal, oil, drugs, etc.) are vital to humanity as foodstuffs, energy sources, engineering and construction materials, and chemicals; and by the way, they shape the environment of the biosphere.
Integrin-mediated Cell Adhesion to Type I Collagen Fibrils
In the integrin family, the collagen receptors form a structurally and functionally distinct subgroup. Two members of this subgroup, α1β1 and α2β1 integrins, are known to bind to monomeric form of type I collagen. However, in tissues type I collagen monomers are organized into large fibrils immediately after they are released from cells. Here, we studied collagen fibril recognition by integrins. By an immunoelectron microscopy method we showed that integrin α2I domain is able to bind to classical D-banded type I collagen fibrils. However, according to the solid phase binding assay, the collagen fibril formation appeared to reduce integrin α1I and α2I domain avidity to collagen and to lower …
Molecular and structural characterization of fluorescent human parvovirus B19 virus-like particles
Although sharing a T = 1 icosahedral symmetry with other members of the Parvoviridae family, it has been suggested that the fivefold channel of the human parvovirus B19 VP2 capsids is closed at its outside end. To investigate the possibility of placing a relatively large protein moiety at this site of B19, fluorescent virus-like particles (fVLPs) of B19 were developed. The enhanced green fluorescent protein (EGFP) was inserted at the N-terminus of the structural protein VP2 and assembly of fVLPs from this fusion protein was obtained. Electron microscopy revealed that these fluorescent protein complexes were very similar in size when compared to wild-type B19 virus. Further, fluorescence cor…
BioImageXD: an open, general-purpose and high-throughput image-processing platform
BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes. We demonstrate its performance in a study of integrin clustering in response to selected inhibitors.
Exploratory nuclear microprobe data visualisation using 3- and 4-dimensional biological volume rendering tools
Abstract The emergence of Confocal Microscopy (CM) and Atomic Force Microscopy (AFM) as everyday tools in cellular level biology has stimulated development of 3D data visualisation software. Conventional 2-dimensional images of cell (optical) sections obtained in a transmission electron or optical microscopes and more sophisticated multidimensional imaging methods require processing software capable of 3D rendering and mathematically transforming data in 3-, 4-, or more dimensions. The richness of data obtained from the different nuclear microscopy imaging techniques and often parallel information channels (X-ray, secondary electron, Scanning Transmission Ion Microscopy) is often not obviou…
BioImageXD - Free Microscopy Image Processing Software
Extended abstract of a paper presented at Microscopy and Microanalysis 2008 in Albuquerque, New Mexico, USA, August 3 – August 7, 2008
The collagen receptor subfamily of the integrins
The four collagen receptor integrins, alpha1beta1, alpha2beta1, alpha10beta1 and alpha11beta1, form a structurally and functionally distinct subgroup when compared to other members of the integrin family. In this review, we discuss the structures of these receptors and their differences in collagen binding and signalling function.
Disassembly of structurally modified viral nanoparticles: characterization by fluorescence correlation spectroscopy.
Abstract Analysis of the breakdown products of engineered viral particles can give useful information on the particle structure. We used various methods to breakdown both a recombinant enveloped virus and virus-like particles (VLPs) from two non-enveloped viruses and analysed the resulting subunits by fluorescence correlation spectroscopy (FCS). Analysis of the enveloped baculovirus, Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV), displaying the green fluorescent protein (GFP) fused to its envelope protein gp64 was performed in the presence and absence of 5 mM SDS and 25 mM DTT. Without treatment, the viral particle showed a diffusion time of 3.3 ms. In the presence of SDS…
Molecular mechanism of α2β1 integrin interaction with human echovirus 1
Conformational activation increases the affinity of integrins to their ligands. On ligand binding, further changes in integrin conformation elicit cellular signalling. Unlike any of the natural ligands of alpha2beta1 integrin, human echovirus 1 (EV1) seemed to bind more avidly a 'closed' than an activated 'open' form of the alpha2I domain. Furthermore, a mutation E336A in the alpha2 subunit, which inactivated alpha2beta1 as a collagen receptor, enhanced alpha2beta1 binding to EV1. Thus, EV1 seems to recognize an inactive integrin, and not even the virus binding could trigger the conformational activation of alpha2beta1. This was supported by the fact that the integrin clustering by EV1 did …
Tetravalent single-chain avidin: from subunits to protein domains via circularly permuted avidins
scAvd (single-chain avidin, where two dcAvd are joined in a single polypeptide chain), having four biotin-binding domains, was constructed by fusion of topologically modified avidin units. scAvd showed similar biotin binding and thermal stability properties as chicken avidin. The DNA construct encoding scAvd contains four circularly permuted avidin domains, plus short linkers connecting the four domains into a single polypeptide chain. In contrast with wild-type avidin, which contains four identical avidin monomers, scAvd enables each one of the four avidin domains to be independently modified by protein engineering. Therefore the scAvd scaffold can be used to construct spatially and stoich…
Enhanced baculovirus-mediated transduction of human cancer cells by tumor-homing peptides.
ABSTRACT Tumor cells and vasculature offer specific targets for the selective delivery of therapeutic genes. To achieve tumor-specific gene transfer, baculovirus tropism was manipulated by viral envelope modification using baculovirus display technology. LyP-1, F3, and CGKRK tumor-homing peptides, originally identified by in vivo screening of phage display libraries, were fused to the transmembrane anchor of vesicular stomatitis virus G protein and displayed on the baculoviral surface. The fusion proteins were successfully incorporated into budded virions, which showed two- to fivefold-improved binding to human breast carcinoma (MDA-MB-435) and hepatocarcinoma (HepG2) cells. The LyP-1 pepti…