Two decades of Martini: Better beads, broader scope

SJ Marrink, L Monticelli, MN Melo… - Wiley …, 2023 - Wiley Online Library
The Martini model, a coarse‐grained force field for molecular dynamics simulations, has
been around for nearly two decades. Originally developed for lipid‐based systems by the …

[PDF][PDF] Considerations and challenges in studying liquid-liquid phase separation and biomolecular condensates

S Alberti, A Gladfelter, T Mittag - Cell, 2019 - cell.com
Evidence is now mounting that liquid-liquid phase separation (LLPS) underlies the formation
of membraneless compartments in cells. This realization has motivated major efforts to …

Condensation of SEUSS promotes hyperosmotic stress tolerance in Arabidopsis

B Wang, H Zhang, J Huai, F Peng, J Wu, R Lin… - Nature Chemical …, 2022 - nature.com
Osmotic stress imposed by drought and high salinity inhibits plant growth and crop yield.
However, our current knowledge on the mechanism by which plants sense osmotic stress is …

Fluorescent protein lifetimes report densities and phases of nuclear condensates during embryonic stem-cell differentiation

K Joron, JO Viegas, L Haas-Neill, S Bier, P Drori… - Nature …, 2023 - nature.com
Fluorescent proteins (FP) are frequently used for studying proteins inside cells. In advanced
fluorescence microscopy, FPs can report on additional intracellular variables. One variable …

Influence of nonspecific interactions on protein associations: implications for biochemistry in vivo

G Rivas, AP Minton - Annual Review of Biochemistry, 2022 - annualreviews.org
The cellular interior is composed of a variety of microenvironments defined by distinct local
compositions and composition-dependent intermolecular interactions. We review the …

In-cell NMR: Why and how?

FX Theillet, E Luchinat - Progress in Nuclear Magnetic Resonance …, 2022 - Elsevier
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as
early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of …

Weak chemical interactions that drive protein evolution: crowding, sticking, and quinary structure in folding and function

D Guin, M Gruebele - Chemical reviews, 2019 - ACS Publications
In recent years, better instrumentation and greater computing power have enabled the
imaging of elusive biomolecule dynamics in cells, driving many advances in understanding …

Physicochemical homeostasis in bacteria

B Poolman - FEMS Microbiology Reviews, 2023 - academic.oup.com
In living cells, the biochemical processes such as energy provision, molecule synthesis,
gene expression, and cell division take place in a confined space where the internal …

Revealing the hidden sensitivity of intrinsically disordered proteins to their chemical environment

D Moses, F Yu, GM Ginell, NM Shamoon… - The journal of …, 2020 - ACS Publications
Intrinsically disordered protein-regions (IDRs) make up roughly 30% of the human proteome
and are central to a wide range of biological processes. Given a lack of persistent tertiary …

Stability prediction of canonical and non-canonical structures of nucleic acids in various molecular environments and cells

S Takahashi, N Sugimoto - Chemical Society Reviews, 2020 - pubs.rsc.org
Nucleic acids (DNA and RNA) dynamically fold and unfold to exert their functions in cells.
These folding and unfolding behaviours are also the basis for various technical applications …