A mechanistic model of de novo folding initiation during biosynthesis is infer and a complete atomistic description of a co-translational folding pathway is provided by linking the folding nucleus to downstream partially structured intermediates and the native state is provided.
Abstract
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.
All proteins can begin to fold on the ribosome, and many rely on co-translational folding to attain their native conformation. This process is not accounted for using structure prediction algorithms such as AlphaFold and its molecular details remain largely unknown. Here, we develop a hydrogen-deuterium pulse-labeling approach which reveals nascent polypeptide folding at a high level of structural detail and its kinetic coupling with translation. Two proteins exhibit hierarchical folding of structures smaller than a domain during translation. A third protein, however, does not have time to conformationally equilibrate on the ribosome, instead becoming kinetically trapped. This subsequently biases post-translational folding to avoid an aggregation-prone intermediate populated during refolding from denaturant. Our results reveal diverse strategies that promote robust protein folding during non-equilibrium translation.
Amir Bitran, C. Bustamante, Susan Marqusee· bioRxiv· 0 citations
It is concluded that the early emergence of the Rossmann fold reflects the chemical and physical constraints of protein folding, explaining both its profound antiquity and sustained longevity.
Koh Seya, Tatsuya Corlett, Hamza Giaffar et al.· bioRxiv· 0 citations
Together, these results show that designed repeat-protein folding is governed by seed formation, interface propagation, and terminal boundary conditions, and establish intramolecular crosslinking as a strategy for rationally reshaping folding landscapes in designed proteins.
Melanie Weiß, Anna Lisa Heit, L. Milles et al.· bioRxiv· 0 citations
The results establish ρ analysis as a general framework to probe RNA conformational pathways and function and uncover multiple folding pathways and modulation in pathway flux that are readily understood from the energetic properties of the constituent RNA motifs.
Brant Gracia, Sarah E Nielson, Daniel Herschlag et al.· bioRxiv· 0 citations
It is shown that short nucleic acids containing Gquadruplex (G4) structure can also catalyze protein folding and uncovers a previously underappreciated role for nucleic acid in proteostasis and offers a new strategy for studying nucleic acid structure-function relationship at residue level.
This work investigates how protein folding landscapes are altered inside condensates, using the protein α-helix as a model folded domain and develops a chemically specific, residue-resolution model for quantification of α-helical folding and applies it to characterize diverse helices within condensates of varying physicochemical properties.
Nathaniel Hess, Jerelle A. Joseph· Journal of the American Chem...· 0 citations
