It is found that Trp-cage folds primarily (80% of the paths) via a pathway forming the tertiary contacts and the salt-bridge, before helix formation, which is in contrast to previous predictions employing an implicit solvent.
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.
Ivana V. Bukvin, Julian O. Streit, Tomasz Włodarski 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
Together, these insights position conformational dynamics at the center of understanding and engineering the evolutionary logic of protein function, opening the door to study how proteins are tuned to operate under the nonequilibrium conditions of living cells.
Sixto M. Herrera, Elías Manríquez-Benítez, Exequiel Medina· Current Opinion in Structura...· 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 demonstrated that BioEmu can generate plausible conformational ensembles for relatively large, six-and seven-pass membrane proteins, sampling rare states at a fraction of the computational cost of conventional MD simulations, suggesting that AI-based ensemble generation could provide an accessible approach for exploring membrane protein dynamics and complement conventional molecular modelling approaches.
B. Clifton, Adam G Grieve, Robin A. Corey· bioRxiv· 0 citations
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
