Distinguishing features of fold‐switching proteins

D Chakravarty, JW Schafer, LL Porter - Protein Science, 2023 - Wiley Online Library
Though many folded proteins assume one stable structure that performs one function, a
small‐but‐increasing number remodel their secondary and tertiary structures and change …

AlphaFold2 fails to predict protein fold switching

D Chakravarty, LL Porter - Protein Science, 2022 - Wiley Online Library
AlphaFold2 has revolutionized protein structure prediction by leveraging sequence
information to rapidly model protein folds with atomic‐level accuracy. Nevertheless, previous …

Fluid protein fold space and its implications

LL Porter - Bioessays, 2023 - Wiley Online Library
Fold‐switching proteins, which remodel their secondary and tertiary structures in response
to cellular stimuli, suggest a new view of protein fold space. For decades, experimental …

Many dissimilar NusG protein domains switch between α-helix and β-sheet folds

LL Porter, AK Kim, S Rimal, LL Looger… - Nature …, 2022 - nature.com
Folded proteins are assumed to be built upon fixed scaffolds of secondary structure, α-
helices and β-sheets. Experimentally determined structures of> 58,000 non-redundant …

Reframing the protein folding problem: Entropy as organizer

GD Rose - Biochemistry, 2021 - ACS Publications
It has been a long-standing conviction that a protein's native fold is selected from a vast
number of conformers by the optimal constellation of enthalpically favorable interactions. In …

[HTML][HTML] Metamorphic proteins under a computational microscope: lessons from a fold-switching RfaH protein

I Artsimovitch, CA Ramírez-Sarmiento - Computational and Structural …, 2022 - Elsevier
Metamorphic proteins constitute unexpected paradigms of the protein folding problem, as
their sequences encode two alternative folds, which reversibly interconvert within …

Predictable fold switching by the SARS‐CoV‐2 protein ORF9b

LL Porter - Protein Science, 2021 - Wiley Online Library
Extant fold‐switching proteins remodel their secondary structures and change their functions
in response to environmental stimuli. These shapeshifting proteins regulate biological …

Self-assembly behavior and sustained drug release properties of amphiphilic poly (amino acid) s

Z Hu, J Wang, S Han, J Hu, A Reheman - New Journal of Chemistry, 2022 - pubs.rsc.org
In this study, a series of poly (amino acid) s materials with amphiphilic properties were
synthesized by ring-opening polymerization. In specific solvents, macromolecules can self …

[HTML][HTML] Proteomic evidence for amyloidogenic cross-seeding in fibrinaloid microclots

DB Kell, E Pretorius - International Journal of Molecular …, 2024 - pmc.ncbi.nlm.nih.gov
In classical amyloidoses, amyloid fibres form through the nucleation and accretion of protein
monomers, with protofibrils and fibrils exhibiting a cross-β motif of parallel or antiparallel β …

[HTML][HTML] Sequence clustering confounds AlphaFold2

JW Schafer, D Chakravarty, EA Chen, LL Porter - bioRxiv, 2024 - ncbi.nlm.nih.gov
Though typically associated with a single folded state, some globular proteins remodel their
secondary and/or tertiary structures in response to cellular stimuli. AlphaFold2 1 (AF2) …