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Biomedical subjects

David G Lynn

Publications and source records attributed to David G Lynn.

7 recordsLinked to original sources

Exploiting amyloid fibril lamination for nanotube self-assembly.

Fundamental questions about the relative arrangement of the beta-sheet arrays within amyloid fibrils remain central to both its structure and the mechanism of self-assembly. Recent computational analyses suggested that sheet-to-sheet lamination was limited by the length of the strand. On the basis of this hypothesis, a short seven-residue segment of the Alzheimer's disease-related Abeta peptide, Abeta(16-22), was allowed to self-assemble under conditions that maintained the basic amphiphilic character of Abeta. Indeed, the number increased over 20-fold to 130 laminates, giving homogeneous bilayer structures that supercoil into long robust nanotubes. Small-angle neutron scattering and X-ray scattering defined the outer and inner radii of the nanotubes in solution to contain a 44-nm inner cavity with 4-nm-thick walls. Atomic force microscopy and transmission electron microscopy images further confirmed these homogeneous arrays of solvent-filled nanotubes arising from a flat rectangular bilayer, 130 nm wide x 4 nm thick, with each bilayer leaflet composed of laminated beta-sheets. The corresponding backbone H-bonds are along the long axis, and beta-sheet lamination defines the 130-nm bilayer width. This bilayer coils to give the final nanotube. Such robust and persistent self-assembling nanotubes with positively charged surfaces of very different inner and outer curvature now offer a unique, robust, and easily accessible scaffold for nanotechnology.

Amyloid↗

Dynamics and fluidity of amyloid fibrils: a model of fibrous protein aggregates.

A previous experimentally defined model for the fibril formed from the core residues of the beta-amyloid (Abeta) peptides of Alzheimer's disease, 10YEVHHQKLVFFAEDVGSNKGAIIGLM, Abeta(10-35) using spectroscopic and scattering analyses reports on the average structure, benefiting immensely from the homogeneous assembly of Abeta(10-35). However, the energetic constraints that contribute to fibril dynamics and stability remain poorly understood. Here we perform molecular dynamics simulations to extend the structural assignment by providing evidence for a dynamic average ensemble with transient backbone H-bonds and internal solvation contributing to the inherent stability of amyloid fibrils.

Amino Acid Sequence↗

Metal switch for amyloid formation: insight into the structure of the nucleus.

The role of Zn2+ in pre-organizing Abeta(10-21) amyloid formation is shown to preferentially alter the relative rate of fibril nucleation and to have little influence on fibril propagation. Fibril morphology, as determined by small angle neutron scattering (SANS) and transmission electron microscopy (TEM), was unchanged in the presence and absence of Zn2+ in Abeta(10-21), as well as in a series of site-specifically altered variants. The metal-independence of the Abeta(10-21)H13Q peptide suggested that the increase in nucleation rate in Abeta(10-21) is due to Zn2+-mediated inter-sheet interactions, involving both histidine 13 and histidine 14.

Amyloid↗

Ratcheting up vir gene expression in Agrobacterium tumefaciens: coiled coils in histidine kinase signal transduction.

The transmembrane histidine kinase VirA is responsible for the recognition of information from several plant-derived xenognostic signals that control gene transfer between Agrobacterium tumefaciens and its eukaryotic host. As with other histidine autokinases, VirA appears to exist as a homodimer within the inner membrane of the bacterium. In this study, we identify the putative homodimeric coiled-coil-like motifs Helix TM2 (amino acids (aa) 259-288) and Helix C (aa 293-327) within the previously assigned signal input domain. The functional importance of these coiled-coil interactions in signal-mediated VirA activation is investigated by the construction of fusion proteins with the leucine zipper domain of the transcription factor GCN4. Replacement of the membrane-spanning and periplasmic domains of VirA with the GCN4 leucine zipper gave functional proteins with increased signal-induced vir gene expression. When the GCN4 fusion was used to conformationally bias the interface of the Helix C coiled coil, constitutively active chimeras were created. The activity of these constructs was dependent on the interface of the Helix C coiled coil, and a ratchet model is proposed in which VirA activation is achieved by signal-induced switching of the interfaces of the homodimer. Since VirA functions as a transducer and integrates various host cues indirectly, these data highlight its role as an "antenna" for the tumor-inducing (Ti) plasmid, able to monitor the host proteome so as to select for successful xenognostic signaling strategies.

Agrobacterium tumefaciens↗

DNA-catalyzed polymerization.

Native DNA oligomers are shown to be stereoselective catalysts for the polymerization of 5'-amino-3'-acetaldehyde-modified thymidine/adenosine nucleosides through reductive amination. The reaction follows step-growth kinetics to read the encoded sequence and chain-length information in the antiparallel direction. Single mismatches in the template are selected against at a level of >100:1. A method is therefore established to translate biopolymer-encoded information stereoselectively into sequence- and chain-length specific synthetic polymers.

Catalysis↗