Stanislaw, J. | bioRxiv Science

bioRxiv2025

Engineering Biohybrid Mycelium Fibers through Hierarchical Structuring and Biomineralization

Driven by the persistence of microplastics and an overdependence on non-renewable sources, mycelium materials have emerged as alternatives to traditional materials, owing to their sustainable production and versatility. Engineered living materials, composite material systems incorporating biological components to enable function, possess desirable regenerative properties but have yet to be fully applied due to their lack of strength versus synthetic or natural materials. We leverage two strategies used by nature to generate mechanical strength: structural hierarchy and biomineralization. We extrude a bioink composed of alginate and a modified strain of the fungus Aspergillus niger capable of silica mineralization, and modulate the morphology by the growth and processing conditions. Mineralization results in significantly stronger and stiffer dried fibers. We demonstrate their potential as textile materials through twisting and braiding to significantly increase the fracture strain. Our results show that mycelium morphology and mechanics can be tuned through mineralization, growth conditions, and processing.

bioengineering↗

bioRxiv2022

Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock

Computationally designed multi-subunit assemblies have shown considerable promise for a variety of applications, including a new generation of potent vaccines. One of the major routes to such materials is rigid body sequence-independent docking of cyclic oligomers into architectures with point group or lattice symmetries. Current methods for docking and designing such assemblies are tailored to specific classes of symmetry and are difficult to modify for novel applications. Here we describe RPXDock, a fast, flexible, and modular software package for sequence-independent rigid-body protein docking across a wide range of symmetric architectures that is easily customizable for further development. RPXDock uses an efficient hierarchical search and a residue-pair transform (RPX) scoring method to rapidly search through multidimensional docking space. We describe the structure of the software, provide practical guidelines for its use, and describe the available functionalities including a variety of score functions and filtering tools that can be used to guide and refine docking results towards desired configurations. Author SummaryProtein design methodologies are now able to generate, through a stepwise approach, a wide variety of self-assembling protein structures that begin to rival the structural complexity of naturally occurring protein nanomachines. Efficient methods for docking oligomeric protein building blocks in user-defined target symmetries are central to these techniques. We developed RPXDock as a fast and versatile method to systematically dock pre-existing proteins together into a multitude of asymmetrical and symmetrical architectures. RPXdock is also readily extendable to future applications through the addition of new symmetries, score functions, and filtering criteria.

bioengineering↗