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 …

Is target-based drug discovery efficient? Discovery and “off-target” mechanisms of all drugs

A Sadri - Journal of medicinal chemistry, 2023 - ACS Publications
Target-based drug discovery is the dominant paradigm of drug discovery; however, a
comprehensive evaluation of its real-world efficiency is lacking. Here, a manual systematic …

Macromolecular crowding in vitro, in vivo, and in between

G Rivas, AP Minton - Trends in biochemical sciences, 2016 - cell.com
Biochemical processes take place in heterogeneous and highly volume-occupied or
crowded environments that can considerably influence the reactivity and distribution of …

Physicochemical properties of cells and their effects on intrinsically disordered proteins (IDPs)

FX Theillet, A Binolfi, T Frembgen-Kesner… - Chemical …, 2014 - ACS Publications
It has long been axiomatic that a protein's structure determines its function. Intrinsically
disordered proteins (IDPs) and disordered protein regions (IDRs) defy this structure …

Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences

HX Zhou, G Rivas, AP Minton - Annu. Rev. Biophys., 2008 - annualreviews.org
Expected and observed effects of volume exclusion on the free energy of rigid and flexible
macromolecules in crowded and confined systems, and consequent effects of crowding and …

Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm

SR McGuffee, AH Elcock - PLoS computational biology, 2010 - journals.plos.org
A longstanding question in molecular biology is the extent to which the behavior of
macromolecules observed in vitro accurately reflects their behavior in vivo. A number of …

Protein organic chemistry and applications for labeling and engineering in live‐cell systems

Y Takaoka, A Ojida, I Hamachi - … Chemie International Edition, 2013 - Wiley Online Library
The modification of proteins with synthetic probes is a powerful means of elucidating and
engineering the functions of proteins both in vitro and in live cells or in vivo. Herein we …

Thermodynamics of protein destabilization in live cells

J Danielsson, X Mu, L Lang, H Wang, A Binolfi… - Proceedings of the …, 2015 - pnas.org
Although protein folding and stability have been well explored under simplified conditions in
vitro, it is yet unclear how these basic self-organization events are modulated by the …

Soft interactions and crowding

M Sarkar, C Li, GJ Pielak - Biophysical reviews, 2013 - Springer
The intracellular milieu is complex, heterogeneous and crowded—an environment vastly
different from dilute solutions in which most biophysical studies are performed. The crowded …

Quinary structure modulates protein stability in cells

WB Monteith, RD Cohen, AE Smith… - Proceedings of the …, 2015 - pnas.org
Protein quinary interactions organize the cellular interior and its metabolism. Although the
interactions stabilizing secondary, tertiary, and quaternary protein structure are well defined …