Biology subjects

Shimanovich, U.

Publications and source records attributed to Shimanovich, U..

3 recordsLinked to original sources

bioRxiv2024

The Natural Material Evolution and Stage-wise Assembly of Silk Along the Silk Gland

Silk fibers, with their highly ordered structure and mechanically superb properties, are produced in arthropod glands at minimal energy input and ambient conditions, a remarkable feat yet to be achieved synthetically. Due to the high instability and shear sensitivity of the silk protein feedstock, understanding silk fiber formation has been largely limited to in-vitro studies of certain gland sections, offering only a fragmented view of this process. Here, we monitor the whole silk feedstock processing in-situ, at the nano- to micron-scales, through imaging its progressive macromolecular assemblies and phase transitions along the entire Bombyx mori silkworm silk gland. This is done by combining state-of-the-art microscopy techniques, such as cryogenic sample preparation, fixation, and imaging. Our work reveals that fibroin assembles into micron-sized spherical storage "compartments" in the posterior and middle gland sections, a state that ensures its stability and avoids premature fibrillation. These compartments undergo several structural transformations along the gland and eventually disassemble at the entry to the anterior section, before the silk feedstock spinning begins. The spinning itself commences via a series of structural transitions, from the alignment of protein chains in liquid feedstock, through the formation of several fibrillated nano-structures and, in the final stage, a network of cross-linked nano-bundles, which determines the structure and properties of the final microfiber. Importantly, the length of the anterior section of the silk gland enables such gradual and balanced structural transitions. This direct imaging of silks natural formation process can help formulate a template for the transformation of fibrillar proteins into synthetic bio-fibers. DedicationThis work is dedicated to the memory of Dr. Eyal Shimoni, who was a valued colleague and a dear friend. Eyal was a vital part of this research and was essential in shaping its direction. He will be deeply missed for his intellect, mindfulness, creativity, and unwavering dedication to scientific development. Though he is no longer with us, his influence and spirit continue to inspire us in our scientific pursuits. May his passion for discovery and commitment to excellence live on through this work.

biochemistry↗

bioRxiv2023

Sound-mediated nucleation and growth of amyloid fibrils

Mechanical energy, specifically in the form of ultrasound, can induce pressure variations and temperature fluctuations when applied to an aqueous media. These conditions can both positively and negatively affect protein complexes, consequently altering their stability, folding patterns, and self-assembling behavior. Despite much scientific progress, our current understanding of the effects of ultrasound on the self-assembly of amyloidogenic proteins remains limited. In the present study, we demonstrate that when the amplitude of the delivered ultrasonic energy is sufficiently low, it can induce refolding of specific motifs in protein monomers, which is sufficient for primary nucleation; this has been revealed by MD. These ultrasound-induced structural changes are initiated by pressure perturbations and are accelerated by a temperature factor. Furthermore, the prolonged action of low-amplitude ultrasound enables the elongation of amyloid protein nanofibrils directly from natively folded monomeric lysozyme protein, in a controlled manner, until it reaches a critical length. Using solution X-ray scattering, we determined that nanofibrillar assemblies, formed either under the action of sound or from natively fibrillated lysozyme, share identical structural characteristics. Thus, these results provide insights into the effects of ultrasound on fibrillar protein self-assembly and lay the foundation for the potential use of sound energy in protein chemistry. Significance StatementUnderstanding how and why proteins form amyloid fibrils is crucial for research into various diseases, including neurodegeneration. Ultrasound is routinely used in research settings as a tool for generating amyloid seeds (nucleation sites) from mature fibrils, which accelerate the rate of fibril growth. However, ultrasound can have various effects on aqueous media including temperature, extreme shear, and free radicals. Here we show that when the ultrasound parameters are precisely adjusted, they can be utilized as a tool for amyloid growth directly from the natively folded monomers. Thus, it is possible to induce minor changes in the folding of proteins, which trigger nucleation and accelerate amyloid growth. This knowledge lays the foundation for the potential use of sound in protein chemistry.

biochemistry↗

bioRxiv2023

Metal Ions Guide the Production of Silkworm Fibers

Silk fibers unique mechanical properties have made them a desirable material for various applications, from medical to optical materials and even in sensing. Yet, to date, no synthetic method has come close to reproducing this remarkably strong biomaterial due to the complexity and insufficient understanding of the mechanism of silk fiber formation. While ions are known to play a key role in the production of natural silk fiber, how they do so has thus far eluded discovery. Here we report that a broad composition of metal ions guides structural transformations in the silk fibroin protein inside the silkworm silk gland. By using a combination of cryo-electron microscopy techniques coupled with elemental analysis, we followed the changes in the composition and spatial localization of metal ions inside the silk gland. We observed that ions are homogenously dispersed during the initial stages of silk secretion and storage inside the silk gland, but once the fibers are spun, the ions delocalize from the silk fibroin fiber core to the sericin coating gum layer. This shift in ion localization is accompanied by the alignment of protein chains and an increase in silk feedstock viscosity inside the silk gland - changes that make the protein more sensitive to shear and enable the initiation of the liquid-to-solid transition in the silk. Moreover, the selective doping of the spun silk fibers with metal ions modifies their mechanical performance. These findings highlight the importance and the dynamic role of metal ions in the evolution of silk fibers mechanical properties, enhance our understanding of the mechanism of silk fiber formation, and lay the foundations for developing new concepts in biomaterial design.

biochemistry↗