Biology subjects

Cassaignau, A. M. E.

Publications and source records attributed to Cassaignau, A. M. E..

4 recordsLinked to original sources

bioRxiv2026

The initiation of de novo protein folding on the ribosome

How the earliest structure within the unfolded state is formed during biosynthesis on the ribosome and whether it has any consequences for downstream folding remain open questions. Here, we combine 15N paramagnetic relaxation enhancement NMR with all-atom molecular dynamics simulations to characterise the unfolded state of a folding-competent immunoglobulin-like domain on the ribosome at the cusp of folding initiation. We identify three structurally distinct sub-ensembles that differ in compaction and ribosome interactions. Non-native contacts, together with ribosome interactions, likely delay folding, yet their persistence alongside early native-like contacts within a sparsely populated compact sub-ensemble suggests they may also facilitate the formation of a co-translational folding nucleus, whose contacts overlap with those of the downstream intermediates. From these findings we infer a mechanistic model of de novo folding initiation during biosynthesis and, by linking the folding nucleus to downstream partially structured intermediates and the native state, provide a complete atomistic description of a co-translational folding pathway.

biophysics↗

bioRxiv2023

Thermodynamic profiles for co-translational trigger factor function

Molecular chaperones are central to the maintenance of proteostasis in living cells. A key member of this protein family is trigger factor (TF), which acts throughout the protein lifecycle and has a ubiquitous role as the first chaperone encountered by proteins during synthesis. However, our understanding of how TF achieves favourable interactions with such a diverse substrate base remains limited. Here, we use microfluidics to reveal the thermodynamic determinants of this process. We find that TF binding to empty 70S ribosomes is enthalpydriven, with micromolar affinity, while nanomolar affinity is achieved through a favourable entropic contribution for both intrinsically disordered and folding competent nascent chains. These findings suggest a general mechanism for co-translational TF function, which relies on occupation of the exposed TF substrate-binding groove, rather than specific complementarity between chaperone and RNC. These insights add to our wider understanding of how proteins can achieve broad substrate specificity.

biophysics↗

bioRxiv2019

Visualising nascent chain dynamics at the ribosome exit tunnel by cryo-electron microscopy

Ribosomes maintain a healthy cellular proteome by synthesising proteins. The nascent chain (NC), emerges into the cellular milieu via the ribosomal exit tunnel, which is an active component that regulates the NC passage. How the NC dynamics at the exit tunnel affect NC folding remains to be an important question, the answer on which has strong implications to medicine. Here, we report high-resolution cryo-EM maps of ribosome nascent-chain complexes (RNCs) displaying distinct steps during biosynthesis. These RNC structures reveal a range of pathways adopted by the NC. The most pronounced diversity in the NC trajectories were found in the vestibule region. Rearrangements of several ribosomal components further suggest that these elements may actively monitor the emerging NC during translation. The ribosome-NC contacts within the vestibule define these NC pathways and modulate position of a folded immunoglobulin domain outside the ribosome.

biophysics↗

bioRxiv2017

Systematic mapping of the free energy landscapes of a growing immunoglobulin domain identifies a kinetic intermediate associated with co-translational proline isomerization

Co-translational folding is a fundamental molecular process that ensures efficient protein biosynthesis and minimizes the wasteful or hazardous formation of misfolded states. However, the complexity of this process makes it extremely challenging to obtain structural characterizations of co-translational folding pathways. Here we contrast observations in translationally-arrested nascent chains with those of a systematic C-terminal truncation strategy. We create a detailed description of chain length-dependent free energy landscapes associated with folding of the FLN5 filamin domain, in isolation and on the ribosome. By using this approach we identify and characterize two folding intermediates, including a partially folded intermediate associated with the isomerization of a conserved proline residue, which, together with measurements of folding kinetics, raises the prospect that neighboring unfolded domains might accumulate during biosynthesis. We develop a simple model to quantify the risk of misfolding in this situation, and show that catalysis of folding by peptidyl-prolyl isomerases is essential to eliminate this hazard.

biophysics↗