What macromolecular crowding can do to a protein

IM Kuznetsova, KK Turoverov, VN Uversky - International journal of …, 2014 - mdpi.com
The intracellular environment represents an extremely crowded milieu, with a limited amount
of free water and an almost complete lack of unoccupied space. Obviously, slightly salted …

Dehydration entropy drives liquid-liquid phase separation by molecular crowding

S Park, R Barnes, Y Lin, B Jeon, S Najafi… - Communications …, 2020 - nature.com
Complex coacervation driven liquid-liquid phase separation (LLPS) of biopolymers has
been attracting attention as a novel phase in living cells. Studies of LLPS in this context are …

Reaching new levels of realism in modeling biological macromolecules in cellular environments

M Feig, Y Sugita - Journal of Molecular Graphics and Modelling, 2013 - Elsevier
An increasing number of studies are aimed at modeling cellular environments in a
comprehensive and realistic fashion. A major challenge in these efforts is how to bridge …

The Golgi-resident protein ACBD3 concentrates STING at ER-Golgi contact sites to drive export from the ER

K Motani, N Saito-Tarashima, K Nishino, S Yamauchi… - Cell Reports, 2022 - cell.com
STING, an endoplasmic reticulum (ER)-resident receptor for cyclic di-nucleotides (CDNs), is
essential for innate immune responses. Upon CDN binding, STING moves from the ER to …

Transcription and translation in cytomimetic protocells perform most efficiently at distinct macromolecular crowding conditions

MA Vibhute, MH Schaap, RJM Maas… - ACS Synthetic …, 2020 - ACS Publications
The formation of cytomimetic protocells that capture the physicochemical aspects of living
cells is an important goal in bottom-up synthetic biology. Here, we recreated the crowded …

Precise timing of ERK phosphorylation/dephosphorylation determines the outcome of trial repetition during long-term memory formation

NV Kukushkin, T Tabassum… - Proceedings of the …, 2022 - National Acad Sciences
Two-trial learning in Aplysia reveals nonlinear interactions between training trials: A single
trial has no effect, but two precisely spaced trials induce long-term memory. Extracellularly …

Oncogenic mutant RAS signaling activity is rescaled by the ERK/MAPK pathway

TE Gillies, M Pargett, JM Silva… - Molecular systems …, 2020 - embopress.org
Activating mutations in RAS are present in~ 30% of human tumors, and the resulting
aberrations in ERK/MAPK signaling play a central role in oncogenesis. However, the form of …

Architecture of the MKK6-p38α complex defines the basis of MAPK specificity and activation

P Juyoux, I Galdadas, D Gobbo, J von Velsen… - Science, 2023 - science.org
The mitogen-activated protein kinase (MAPK) p38α is a central component of signaling in
inflammation and the immune response and is, therefore, an important drug target. Little is …

On the parameter combinations that matter and on those that do not: data-driven studies of parameter (non) identifiability

N Evangelou, NJ Wichrowski, GA Kevrekidis… - PNAS …, 2022 - academic.oup.com
We present a data-driven approach to characterizing nonidentifiability of a model's
parameters and illustrate it through dynamic as well as steady kinetic models. By employing …

DNA binding proteins explore multiple local configurations during docking via rapid rebinding

M Ganji, M Docter, SFJ Le Grice… - Nucleic acids …, 2016 - academic.oup.com
Finding the target site and associating in a specific orientation are essential tasks for DNA-
binding proteins. In order to make the target search process as efficient as possible, proteins …