The molecular basis for cellular function of intrinsically disordered protein regions

AS Holehouse, BB Kragelund - Nature Reviews Molecular Cell Biology, 2024 - nature.com
Intrinsically disordered protein regions exist in a collection of dynamic interconverting
conformations that lack a stable 3D structure. These regions are structurally heterogeneous …

Molecular dynamics simulations in drug discovery and pharmaceutical development

OMH Salo-Ahen, I Alanko, R Bhadane, AMJJ Bonvin… - Processes, 2020 - mdpi.com
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug
development process. In this review, we give a broad overview of the current application …

AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination

TC Terwilliger, D Liebschner, TI Croll, CJ Williams… - Nature …, 2024 - nature.com
Artificial intelligence-based protein structure prediction methods such as AlphaFold have
revolutionized structural biology. The accuracies of these predictions vary, however, and …

EffectorP 3.0: prediction of apoplastic and cytoplasmic effectors in fungi and oomycetes

J Sperschneider, PN Dodds - Molecular plant-microbe …, 2022 - Am Phytopath Society
Many fungi and oomycete species are devasting plant pathogens. These eukaryotic
filamentous pathogens secrete effector proteins to facilitate plant infection. Fungi and …

CAMPR4: a database of natural and synthetic antimicrobial peptides

U Gawde, S Chakraborty, FH Waghu… - Nucleic Acids …, 2023 - academic.oup.com
There has been an exponential increase in the design of synthetic antimicrobial peptides
(AMPs) for its use as novel antibiotics. Synthetic AMPs are substantially enriched in residues …

Deubiquitinase-targeting chimeras for targeted protein stabilization

NJ Henning, L Boike, JN Spradlin, CC Ward… - Nature chemical …, 2022 - nature.com
Many diseases are driven by proteins that are aberrantly ubiquitinated and degraded. These
diseases would be therapeutically benefited by targeted protein stabilization (TPS). Here we …

Intrinsically disordered proteins and their “mysterious”(meta) physics

VN Uversky - Frontiers in Physics, 2019 - frontiersin.org
Recognition of the natural abundance and functional importance of intrinsically disordered
proteins (IDPs), and protein hybrids that contain both intrinsically disordered protein regions …

Improved AlphaFold modeling with implicit experimental information

TC Terwilliger, BK Poon, PV Afonine, CJ Schlicksup… - Nature …, 2022 - nature.com
Abstract Machine-learning prediction algorithms such as AlphaFold and RoseTTAFold can
create remarkably accurate protein models, but these models usually have some regions …

Intrinsically disordered proteins: an overview

R Trivedi, HA Nagarajaram - International journal of molecular sciences, 2022 - mdpi.com
Many proteins and protein segments cannot attain a single stable three-dimensional
structure under physiological conditions; instead, they adopt multiple interconverting …

Intrinsically disordered proteins in overcrowded milieu: Membrane-less organelles, phase separation, and intrinsic disorder

VN Uversky - Current opinion in structural biology, 2017 - Elsevier
Highlights•Eukaryotic cells are inhomogeneously crowded and contain various cellular
bodies.•Some of these bodies are proteinaceous membrane-less organelles …