PhD project

Supervisors: Anthony Roberts & Katarina Toropova

How are membrane proteins trafficked within cells with such speed and precision? Our research aims to address this question by uncovering the molecular mechanisms of cargo transport by microtubule-based motor proteins, with a particular focus on the formation and function of the primary cilium.

The primary cilium is a microtubule-based, antenna-like organelle present on nearly every cell in the human body. It plays a crucial role in sensing and transducing environmental signals to guide cell behaviour during development. Disruption of ciliary trafficking pathways leads to a range of severe developmental and degenerative diseases, collectively known as ciliopathies.

A key challenge in this process is the trafficking of transmembrane receptors into and out of the cilium. We recently determined the cryo-EM structure of the IFT-A complex – a multiprotein assembly essential for this function – and used CRISPR/Cas9 genome editing to dissect its role [1]. IFT-A forms a polymeric, multi-megadalton ‘train’ that links transmembrane cargoes to kinesin-2 and dynein-2 motor proteins for bidirectional transport along microtubules [2–4].

The central goal of this PhD project is to determine how IFT-A recognizes and transports a wide array of membrane proteins, despite their apparent lack of sequence similarity.

To achieve this, the project will combine state-of-the-art techniques, including:

· Cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET)

· Live-cell fluorescence microscopy

· CRISPR-based genetic tools

· Proteome-wide interaction screening using AlphaFold

This project offers an opportunity to work at the interface of structural biology, cell biology, and computational biology, with the potential to uncover fundamental mechanisms relevant to human health and disease.

Keywords:

• Biochemistry, Biophysics, Cell Biology/Development, Molecular Biology, Structural Biology

Publications:

1. IFT-A Structure Reveals Carriages for Membrane Protein Transport into Cilia (2022) Hesketh SJ, Mukhopadhyay AG, Nakamura D, Toropova K, Roberts AJ. Cell, 185(26):4971-4985
2. Regulation of kinesin-2 motility by its β-hairpin motif (2025) Webb S, Toropova K, Mukhopadhyay AG, Nofal SD, Roberts AJ. Nature Structural & Molecular Biology (in press)
3. Toropova K, Zalyte R, Mukhopadhyay AG, Mladenov M, Carter AP, Roberts AJ (2019) Structure of the Dynein-2 Complex and its Assembly with Intraflagellar Transport Trains. Nature Structural & Molecular Biology, 26(9):823-829
4. Intraflagellar Transport Trains and Motors (2020) Webb S, Mukhopadhyay AG, Roberts AJ. Seminars in Cell & Developmental Biology, 107:82-90