Fuzziness and frustration in the energy landscape of protein folding, function, and assembly

S Gianni, MI Freiberger, P Jemth… - Accounts of chemical …, 2021 - ACS Publications
Conspectus Are all protein interactions fully optimized? Do suboptimal interactions
compromise specificity? What is the functional impact of frustration? Why does evolution not …

[HTML][HTML] Binding mechanisms of intrinsically disordered proteins: Insights from experimental studies and structural predictions

T Orand, MR Jensen - Current Opinion in Structural Biology, 2025 - Elsevier
Advances in the characterization of intrinsically disordered proteins (IDPs) have unveiled a
remarkably complex and diverse interaction landscape, including coupled folding and …

The mechanism of amyloid fibril growth from Φ-value analysis

JA Larsen, A Barclay, N Vettore, LK Klausen… - Nature Chemistry, 2025 - nature.com
Amyloid fibrils are highly stable misfolded protein assemblies that play an important role in
several neurodegenerative and systemic diseases. Although structural information of the …

[HTML][HTML] Protein dynamics: The future is bright and complicated!

K Nam, M Wolf-Watz - Structural Dynamics, 2023 - pubs.aip.org
Biological life depends on motion, and this manifests itself in proteins that display motion
over a formidable range of time scales spanning from femtoseconds vibrations of atoms at …

Evolutionary fine-tuning of residual helix structure in disordered proteins manifests in complex structure and lifetime

S Elkjær, AD Due, LF Christensen, FF Theisen… - Communications …, 2023 - nature.com
Transcription depends on complex networks, where folded hub proteins interact with
intrinsically disordered transcription factors undergoing coupled folding and binding. For …

[HTML][HTML] Disordered regions flanking the binding interface modulate affinity between CBP and NCOA

E Karlsson, J Schnatwinkel, C Paissoni… - Journal of Molecular …, 2022 - Elsevier
Recognition motifs that mediate protein–protein interactions are usually embedded within
longer intrinsically disordered regions. While binding interfaces involving the recognition …

[HTML][HTML] Unveiling induced folding of intrinsically disordered proteins–Protein engineering, frustration and emerging themes

F Malagrinò, A Diop, L Pagano, C Nardella… - Current Opinion in …, 2022 - Elsevier
Intrinsically disordered proteins (IDPs) can be generally described as a class of proteins that
lack a well-defined ordered structure in isolation at physiological conditions. Upon binding to …

The transition state for coupled folding and binding of a disordered DNA binding domain resembles the unbound state

M Kuravsky, C Kelly, C Redfield… - Nucleic Acids …, 2024 - academic.oup.com
The basic zippers (bZIPs) are one of two large eukaryotic families of transcription factors
whose DNA binding domains are disordered in isolation but fold into stable α-helices upon …

[HTML][HTML] Protein binding and folding through an evolutionary lens

P Jemth - Current Opinion in Structural Biology, 2025 - Elsevier
Protein–protein associations are often mediated by an intrinsically disordered protein region
interacting with a folded domain in a coupled binding and folding reaction. Classic physical …

Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering

MJ Bakker, A Gaffour, M Juhás, V Zapletal… - Journal of Chemical …, 2024 - ACS Publications
By merging advanced dimensionality reduction (DR) and clustering algorithm (CA)
techniques, our study advances the sampling procedure for predicting NMR chemical shifts …