Physics-based computational and theoretical approaches to intrinsically disordered proteins

JE Shea, RB Best, J Mittal - Current opinion in structural biology, 2021 - Elsevier
Highlights•Liquid-liquid phase separation underlies the formation of membraneless
organelles within cells.•Theory and molecular simulations help to relate interactions at the …

Global structure of the intrinsically disordered protein tau emerges from its local structure

LS Stelzl, LM Pietrek, A Holla, J Oroz, M Sikora… - Jacs Au, 2022 - ACS Publications
The paradigmatic disordered protein tau plays an important role in neuronal function and
neurodegenerative diseases. To disentangle the factors controlling the balance between …

Intrinsically disordered proteins: ensembles at the limits of Anfinsen's dogma

P Kulkarni, VBP Leite, S Roy, S Bhattacharyya… - Biophysics …, 2022 - pubs.aip.org
Intrinsically disordered proteins (IDPs) are proteins that lack rigid 3D structure. Hence, they
are often misconceived to present a challenge to Anfinsen's dogma. However, IDPs exist as …

Tuning protein hydrogel mechanics through modulation of nanoscale unfolding and entanglement in postgelation relaxation

MDG Hughes, S Cussons, N Mahmoudi, DJ Brockwell… - ACS …, 2022 - ACS Publications
Globular folded proteins are versatile nanoscale building blocks to create biomaterials with
mechanical robustness and inherent biological functionality due to their specific and well …

Integrating single-molecule spectroscopy and simulations for the study of intrinsically disordered proteins

JJ Alston, A Soranno, AS Holehouse - Methods, 2021 - Elsevier
Over the last two decades, intrinsically disordered proteins and protein regions (IDRs) have
emerged from a niche corner of biophysics to be recognized as essential drivers of cellular …

Mapping the Multiscale Proteomic Organization of Cellular and Disease Phenotypes

A Cesnik, LV Schaffer, I Gaur, M Jain… - Annual Review of …, 2024 - annualreviews.org
While the primary sequences of human proteins have been cataloged for over a decade,
determining how these are organized into a dynamic collection of multiprotein assemblies …

Data-driven models for predicting intrinsically disordered protein polymer physics directly from composition or sequence

TH Chao, S Rekhi, J Mittal, DP Tabor - Molecular Systems Design & …, 2023 - pubs.rsc.org
The molecular-level understanding of intrinsically disordered proteins is challenging due to
experimental characterization difficulties. Computational understanding of IDPs also …

Intrinsically disordered proteins at the nano-scale

T Ehm, H Shinar, S Meir, A Sekhon, V Sethi… - Nano …, 2021 - iopscience.iop.org
The human proteome is enriched in proteins that do not fold into a stable 3D structure.
These intrinsically disordered proteins (IDPs) spontaneously fluctuate between a large …

How much can physics do for protein design?

E Michael, T Simonson - Current Opinion in Structural Biology, 2022 - Elsevier
Physics and physical chemistry are an important thread in computational protein design,
complementary to knowledge-based tools. They provide molecular mechanics scoring …

Proline isomerization regulates the phase behavior of elastin-like polypeptides in water

Y Zhao, K Kremer - The Journal of Physical Chemistry B, 2021 - ACS Publications
Responsiveness of polypeptides and polymers in aqueous solution plays an important role
in biomedical applications and in designing advanced functional materials. Elastin-like …