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The European High Performance Computing Joint Undertaking (EuroHPC JU)

Computational Microscopy: in-cell co-translational folding and misfolding in health and disease

Awarded Resources (in core hours)
System Partition
1 November 2022 - 31 October 2023
Allocation Period

Most proteins in the cell begin to fold co-translationally on the ribosome while they emerge from its exit tunnel. A growing amount of evidence also demonstrates that the ribosome itself can significantly modulate this process.

Understanding the co-translational protein folding (CTF) is critical for proteostasis, protein complex assembly or misfolding, which can be linked to many devastating conditions such as cystic fibrosis, alpha-1 antitrypsin (AAT) deficiency, lysozyme amyloidosis, Parkinson’s and Alzheimer’s. Despite its importance, surprisingly little is known structurally about co-translational folding mechanisms, particularly of the folding intermediate species involved.

This is partly due to the experimental challenges in obtaining high-resolution structural data: while we have pioneered the structural analysis of elongating nascent polypeptides – via ribosome nascent chain complexes (RNCs), these analyses are time-intensive experimental processes that require careful selection of the ‘snapshot’ of translation to study.

The combination of cryo-EM and NMR has proven particularly powerful at providing the most detailed structural information on the nascent polypeptide during its CTF. However, NMR is challenging even on isolated systems that exceed ca. 50 kDa and CTF studies of such a larger system in the presence of the ribosome is a major undertaking. Meanwhile, cryo-EM is limited to low-resolution maps of nascent chain, and many transiently-populated states are not observed through the dynamics.

Consequently, the use of accurate and efficient computational techniques, such as molecular dynamics (MD) simulations in combination with NMR and cryo-EM experimental data used as restraints or validation, is imperative for a detailed understanding of how proteins fold in the cell.

In this proposal, the goal it to seek to use all-atom molecular dynamics simulations, combined with NMR and cryo-EM data, to study the co-translational folding process for several relevant polypeptide systems, including aggregation-prone.

The project aims at characterising the complete free energy landscape, including the folding intermediates states that can be in the future targeted by design binders to prevent or increase CTF. Due to the multi-million atom system size of the ribosomal nascent chain complexes and the timescales associated with protein folding(μs-s), these systems are only accessible to MD simulations on the most powerful HPCs like LUMI.