Research Highlight: From de novo design of higher order complexes to a random protein walker
Powered protein motors such as kinesin, dynein, and myosin drive intracellular transport and movement by walking along cytoskeletal filaments. While recent advances in deep learning have significantly improved the success of de novo protein design, the creation of large, dynamic protein machines remains a major challenge.
In this talk, Ajasja Ljubetič will present the design and experimental characterisation of a synthetic protein walker capable of diffusing along micrometer-scale protein fibres. This system represents a key step toward the development of engineered molecular machines.
The design is based on three essential components: a track, attachment interfaces, and a walker scaffold. He will describe how de novo–designed fibres were constructed using rigidly fused heterodimers and designed helical repeat proteins, and will present their experimental validation through cryo-electron microscopy (cryo-EM).
The talk will further introduce a range of walker scaffolds with varying numbers of “feet,” along with their experimentally determined structures. Using single-molecule TIRF microscopy, the team observed that walkers with more attachment points exhibit increased mobility, revealing key design principles for future programmable protein-based machines.
About Prof. Ajasja Ljubetič
Ajasja Ljubetič is a Research Assistant Professor and group leader at the National Institute of Chemistry Slovenia, within the Department of Synthetic Biology and Immunology.
His research focuses on the design of dynamic proteins and molecular machines, combining the Rosetta platform with state-of-the-art deep learning approaches. His group is developing accessible tools for de novo protein design, including the Prosculpt pipeline, with the aim of making protein engineering more accessible to non-computational scientists.
Dr. Ljubetič was awarded a Marie Skłodowska-Curie Global Fellowship, during which he trained in protein design in the laboratory of David Baker. He is currently the recipient of an ERC Consolidator Grant (PROPEL), focused on engineering protein-based molecular machines. More information about his research is available at https://ljubetic-lab.si/.