Computational approaches to predict protein–protein interactions in crowded cellular environments

G Grassmann, M Miotto, F Desantis… - Chemical …, 2024 - ACS Publications
Investigating protein–protein interactions is crucial for understanding cellular biological
processes because proteins often function within molecular complexes rather than in …

Macromolecular crowding is more than hard-core repulsions

SL Speer, CJ Stewart, L Sapir… - Annual Review of …, 2022 - annualreviews.org
Cells are crowded, but proteins are almost always studied in dilute aqueous buffer. We
review the experimental evidence that crowding affects the equilibrium thermodynamics of …

Crowding in cellular environments at an atomistic level from computer simulations

M Feig, I Yu, P Wang, G Nawrocki… - The Journal of Physical …, 2017 - ACS Publications
The effects of crowding in biological environments on biomolecular structure, dynamics, and
function remain not well understood. Computer simulations of atomistic models of …

Effects of proteins on protein diffusion

Y Wang, C Li, GJ Pielak - Journal of the American Chemical …, 2010 - ACS Publications
Despite increased attention, little is known about how the crowded intracellular environment
affects basic phenomena like protein diffusion. Here, we use NMR to quantify the rotational …

In-cell thermodynamics and a new role for protein surfaces

AE Smith, LZ Zhou, AH Gorensek, M Senske… - Proceedings of the …, 2016 - pnas.org
There is abundant, physiologically relevant knowledge about protein cores; they are
hydrophobic, exquisitely well packed, and nearly all hydrogen bonds are satisfied. An …

The molecular mechanism of nuclear transport revealed by atomic-scale measurements

LE Hough, K Dutta, S Sparks, DB Temel, A Kamal… - Elife, 2015 - elifesciences.org
Nuclear pore complexes (NPCs) form a selective filter that allows the rapid passage of
transport factors (TFs) and their cargoes across the nuclear envelope, while blocking the …

Protein 19F NMR in Escherichia coli

C Li, GF Wang, Y Wang, R Creager-Allen… - Journal of the …, 2010 - ACS Publications
Although overexpression and 15N enrichment facilitate the observation of resonances from
disordered proteins in Escherichia coli, 15N enrichment alone is insufficient for detecting …

The more the merrier: effects of macromolecular crowding on the structure and dynamics of biological membranes

M Löwe, M Kalacheva, AJ Boersma… - The FEBS …, 2020 - Wiley Online Library
Proteins are essential and abundant components of cellular membranes. Being densely
packed within the limited surface area, proteins fulfil essential tasks for life, which include …

Slow-down in diffusion in crowded protein solutions correlates with transient cluster formation

G Nawrocki, P Wang, I Yu, Y Sugita… - The Journal of Physical …, 2017 - ACS Publications
For a long time, the effect of a crowded cellular environment on protein dynamics has been
largely ignored. Recent experiments indicate that proteins diffuse more slowly in a living cell …

Protein folding in the cell: challenges and progress

A Gershenson, LM Gierasch - Current opinion in structural biology, 2011 - Elsevier
It is hard to imagine a more extreme contrast than that between the dilute solutions used for
in vitro studies of protein folding and the crowded, compartmentalized, sticky, spatially …