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 …

Understanding hydrophobic effects: Insights from water density fluctuations

NB Rego, AJ Patel - Annual Review of Condensed Matter …, 2022 - annualreviews.org
The aversion of hydrophobic solutes for water drives diverse interactions and assemblies
across materials science, biology, and beyond. Here, we review the theoretical …

[HTML][HTML] Conformational stability and denaturation processes of proteins investigated by electrophoresis under extreme conditions

P Masson, S Lushchekina - Molecules, 2022 - mdpi.com
The functional structure of proteins results from marginally stable folded conformations.
Reversible unfolding, irreversible denaturation, and deterioration can be caused by …

Role of computational methods in going beyond X-ray crystallography to explore protein structure and dynamics

A Srivastava, T Nagai, A Srivastava… - International journal of …, 2018 - mdpi.com
Protein structural biology came a long way since the determination of the first three-
dimensional structure of myoglobin about six decades ago. Across this period, X-ray …

Reversible switching between two common protein folds in a designed system using only temperature

TL Solomon, Y He, N Sari, Y Chen… - Proceedings of the …, 2023 - pnas.org
Naturally occurring metamorphic proteins have the ability to interconvert from one folded
state to another through either a limited set of mutations or by way of a change in the local …

[HTML][HTML] Studying rare events using forward-flux sampling: Recent breakthroughs and future outlook

S Hussain, A Haji-Akbari - The Journal of Chemical Physics, 2020 - pubs.aip.org
Rare events are processes that occur upon the emergence of unlikely fluctuations. Unlike
what their name suggests, rare events are fairly ubiquitous in nature, as the occurrence of …

Environmental factors modulating protein conformations and their role in protein aggregation diseases

S Devi, M Chaturvedi, S Fatima, S Priya - Toxicology, 2022 - Elsevier
The adverse physiological conditions have been long known to impact protein synthesis,
folding and functionality. Major physiological factors such as the effect of pH, temperature …

Towards molecular movies with X-ray photon correlation spectroscopy

F Perakis, C Gutt - Physical Chemistry Chemical Physics, 2020 - pubs.rsc.org
In this perspective article we highlight research opportunities and challenges in probing
structural dynamics of molecular systems using X-ray Photon Correlation Spectroscopy …

Probing the non-covalent forces key to the thermodynamics of β-hairpin unfolding

TH Tran, P Prusty, M Ricciardi, CR Travis… - Chemical …, 2024 - pubs.rsc.org
Although it is well understood that the graph of the free energy of unfolding (ΔG) of a
globular protein with temperature approximates to a negative parabola, there is as yet no …

Insights into the effects of different drying methods on protein oxidation and degradation characteristics of golden pompano (Trachinotus ovatus)

P Chen, Y Qiu, S Chen, Y Zhao, Y Wu, Y Wang - Frontiers in Nutrition, 2022 - frontiersin.org
The quality of dried fish products differs based on the drying method employed owing to the
different drying principles, with changes in protein affecting the quality of these products …