Intrinsically disordered proteins/regions and insight into their biomolecular interactions

P Chakrabarti, D Chakravarty - Biophysical Chemistry, 2022 - Elsevier
Proteins may vary from being rigid to having flexible regions to being completely disordered,
either as an intrinsically disordered protein (IDP) or having specific intrinsically disordered …

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 …

AlphaFold predictions of fold-switched conformations are driven by structure memorization

D Chakravarty, JW Schafer, EA Chen, JF Thole… - Nature …, 2024 - nature.com
Recent work suggests that AlphaFold (AF)–a deep learning-based model that can
accurately infer protein structure from sequence–may discern important features of folded …

High-throughput prediction of protein conformational distributions with subsampled AlphaFold2

G Monteiro da Silva, JY Cui, DC Dalgarno… - nature …, 2024 - nature.com
This paper presents an innovative approach for predicting the relative populations of protein
conformations using AlphaFold 2, an AI-powered method that has revolutionized biology by …

Design of stimulus-responsive two-state hinge proteins

F Praetorius, PJY Leung, MH Tessmer, A Broerman… - Science, 2023 - science.org
In nature, proteins that switch between two conformations in response to environmental
stimuli structurally transduce biochemical information in a manner analogous to how …

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 …

[HTML][HTML] AlphaFold2 has more to learn about protein energy landscapes

D Chakravarty, JW Schafer, EA Chen, JR Thole… - BioRxiv, 2023 - ncbi.nlm.nih.gov
Recent work suggests that AlphaFold2 (AF2)–a deep learning-based model that can
accurately infer protein structure from sequence–may discern important features of folded …

[HTML][HTML] Protein representations: Encoding biological information for machine learning in biocatalysis

D Harding-Larsen, J Funk, NG Madsen… - Biotechnology …, 2024 - Elsevier
Enzymes offer a more environmentally friendly and low-impact solution to conventional
chemistry, but they often require additional engineering for their application in industrial …

[HTML][HTML] Design and discovery of metamorphic proteins

AF Dishman, BF Volkman - Current opinion in structural biology, 2022 - Elsevier
Metamorphic proteins are single amino acid sequences that reversibly interconvert between
multiple, dramatically different native structures, often with distinct functions. Since the …