Effects of molecular crowding on the structures, interactions, and functions of nucleic acids

S Nakano, D Miyoshi, N Sugimoto - Chemical reviews, 2014 - ACS Publications
Nucleic acids are excellent at recognizing complementary sequences through the formation
of Watson− Crick base pairs. Since the base pairing enables the highly selective …

[HTML][HTML] Formation of protein complexes in crowded environments–from in vitro to in vivo

Y Phillip, G Schreiber - FEBS letters, 2013 - Elsevier
Traditionally, biochemical studies are performed in dilute homogenous solutions, which are
very different from the dense mixture of molecules found in cells. Thus, the physiological …

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 as a regulator of gene transcription

H Matsuda, GG Putzel, V Backman, I Szleifer - Biophysical journal, 2014 - cell.com
Studies of macromolecular crowding have shown its important effects on molecular transport
and interactions in living cells. Less clear is the effect of crowding when its influence is …

Motion of nanoprobes in complex liquids within the framework of the length-scale dependent viscosity model

T Kalwarczyk, K Sozanski, A Ochab-Marcinek… - Advances in colloid and …, 2015 - Elsevier
This paper deals with the recent phenomenological model of the motion of nanoscopic
objects (colloidal particles, proteins, nanoparticles, molecules) in complex liquids. We …

Crowding induced entropy-enthalpy compensation in protein association equilibria

YC Kim, J Mittal - Physical Review Letters, 2013 - APS
A statistical mechanical theory is presented to predict the effects of macromolecular
crowding on protein association equilibria, accounting for both excluded volume and …

Dynamics in crowded environments: is non-Gaussian Brownian diffusion normal?

G Kwon, BJ Sung, A Yethiraj - The Journal of Physical Chemistry …, 2014 - ACS Publications
The dynamics of colloids and proteins in dense suspensions is of fundamental importance,
from a standpoint of understanding the biophysics of proteins in the cytoplasm and for the …

Disordered chromatin packing regulates phenotypic plasticity

RKA Virk, W Wu, LM Almassalha, GM Bauer, Y Li… - Science …, 2020 - science.org
Three-dimensional supranucleosomal chromatin packing plays a profound role in
modulating gene expression by regulating transcription reactions through mechanisms such …

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 …

Proteins from Thermophilic Thermus thermophilus Often Do Not Fold Correctly in a Mesophilic Expression System Such as Escherichia coli

A Kruglikov, Y Wei, X Xia - ACS omega, 2022 - ACS Publications
Majority of protein structure studies use Escherichia coli (E. coli) and other model organisms
as expression systems for other species' genes. However, protein folding depends on …