Nishen Naidoo

Crystal Structure of Lsm3 Octamer from Saccharomyces cerevisiae: Implications for Lsm Ring Organisation and Recruitment

Sm and Sm-like (Lsm) proteins are core components of the ribonucleoprotein complexes essential to key nucleic acid processing events within the eukaryotic cell. They assemble as polyprotein ring scaffolds that have the capacity to bind RNA substrates and other necessary protein factors. The crystal structure of yeast Lsm3 reveals a new organisation of the L/Sm beta-propeller ring, containing eight protein subunits. Little distortion of the characteristic L/Sm fold is required to form the octamer, indicating that the eukaryotic Lsm ring may be more pliable than previously thought. The homomeric Lsm3 octamer is found to successfully recruit Lsm6, Lsm2 and Lsm5 directly from yeast lysate. Our crystal structure shows the C-terminal tail of each Lsm3 subunit to be engaged in connections across rings through specific beta-sheet interactions with elongated loops protruding from neighbouring octamers. While these loops are of distinct length for each Lsm protein and generally comprise low-complexity polar sequences, several Lsm C-termini comprise hydrophobic sequences suitable for beta-sheet interactions. The Lsm3 structure thus provides evidence for protein-protein interactions likely utilised by the highly variable Lsm loops and termini in the recruitment of RNA processing factors to mixed Lsm ring scaffolds. Our coordinates also provide updated homology models for the active Lsm[1-7] and Lsm[2-8] heptameric rings.

Atomic force microscopy of orb-spider-web-silks to measure surface nanostructuring and evaluate silk fibers per strand

Atomic force microscopy (AFM) study is used to measure the surface topology and roughness of radial and capture spider silks on the micro- and nanoscale. This is done for silks of the orb weaver spider Argiope keyserlingi. Capture silk has a surface roughness that is five times less than that for radial silk. The capture silk has an equivalent flatness of λ/100 (5–6 nm deep surface features) as an optical surface. This is equivalent to a very highly polished optical surface. AFM does show the number of silk fibers that make up a silk thread but geometric distortion occurs during sample preparation. This prevented AFM from accurately measuring the silk topology on the microscale in this study.

Optics of spider "sticky" orb webs

Spider orb webs are known to produce colour displays in nature, both in reflection and transmission of sunlight, under certain illumination conditions. The cause of these colours has been the subject of speculation since the time of Newton. It has also been the topic of observational interpretation and some experiment which has proposed diffraction by the fine silks, scattering from rough/structured surfaces and thin film effects as the primary causes. We report systematic studies carried out using the silks of Australian orb web weaving spiders. Studies of both white light and laser light scattering/propagation by natural spider silks have definitively determined the primary cause of the colour displays is rainbows that can be understood by the application of geometric optics combined with new knowledge of the optical properties of the spider web strands, silks, and proteins as optical materials. Additionally, a range of microscopies (optical, AFM, optical surface profiling) show the silks to be optically flat. Overall, spider silks emerge as fascinating optical materials with high dispersion, high birefringence and the potential for future research to show they have high nonlinear optical coefficients. Their importance as a bioinspiration in optics is only just beginning to be realised. Their special optical properties have been achieved by ~136 million years of evolution driven by the need for the web to evade detection by insect prey.

Optical surface profilometry and AFM of Orb weaver spider silks

AFM (Atomic Force Microscopy) and OSP (Optical Surface Profiling) have been applied to measure the surfaces of spider silks — both radials and capture silks- at the nano- and micro-scale.

Micro-optical elements and optical materials of certain spider webs

Certain spider webs are composed of several types of micro-optical elements made from transparent optical materials. The silks (radial and capture) are almost exclusively protein. The nearly cylindrical silks have diameters in the range 0.1 to several microns and cross-sectional morphology that is cylindrical-multi-layered,.as studied by transmission electron microscopy, The capture threads are coated with aqueous adhesive that also forms into nearly elliptical micro-lenses (adhesive droplets) mounted on the near cylindrical silks. The remaining elements of the web are the cement junctions tying the radial and the capture threads of the web together. These are irregularly shaped platelets. Progress to date on our research characterizing the optical properties and function of these transparent orb webs has been to interpret the reflection and transmission properties of the elements of the web, and the web as a whole, in natural lighting; to evaluate the optical finish of the surface of the silks and capture droplets; and to measure the principal refractive indices of radial silks using new immersion based methods developed for application to micron-sized, curved optical elements. Here we report the principal refractive indices, birefringence, dispersion and morphology of transparent spider silk subject to various chemical treatments. The morphology is measured using TEM. Insight into the physical origin of the refractive index properties will be discussed.