Molecular and environmental determinants of biomolecular condensate formation

JA Villegas, M Heidenreich, ED Levy - Nature chemical biology, 2022 - nature.com
Biomolecular condensate formation has been implicated in a host of biological processes
and has found relevance in biology and disease. Understanding the physical principles and …

[HTML][HTML] Diffusive intracellular interactions: On the role of protein net charge and functional adaptation

EV Estrada, N Zhang, H Wennerström… - Current opinion in …, 2023 - Elsevier
A striking feature of nucleic acids and lipid membranes is that they all carry net negative
charge and so is true for the majority of intracellular proteins. It is suggested that the role of …

Analytical formulation and field-theoretic simulation of sequence-specific phase separation of protein-like heteropolymers with short-and long-spatial-range …

J Wessén, S Das, T Pal, HS Chan - The Journal of Physical …, 2022 - ACS Publications
A theory for sequence-dependent liquid–liquid phase separation (LLPS) of intrinsically
disordered proteins (IDPs) in the study of biomolecular condensates is formulated by …

Rational Tuning of the Concentration-independent Enrichment of Prion-like Domains in Stress Granules

MH Baer, SM Cascarina, KR Paul, ED Ross - Journal of Molecular Biology, 2024 - Elsevier
Stress granules (SGs) are large ribonucleoprotein assemblies that form in response to acute
stress in eukaryotes. SG formation is thought to be initiated by liquid–liquid phase …

Seq2Phase: language model-based accurate prediction of client proteins in liquid–liquid phase separation

K Miyata, W Iwasaki - Bioinformatics Advances, 2024 - academic.oup.com
Motivation Liquid–liquid phase separation (LLPS) enables compartmentalization in cells
without biological membranes. LLPS plays essential roles in membraneless organelles such …

Come for the atmosphere, stay for the interactions: Deciphering small molecule partitioning into biomolecular condensates

B Sepehri, K Drew, JA Villegas - Cell Chemical Biology, 2023 - cell.com
Optimizing pharmacokinetic properties remains challenging but is generally guided by a set
of structural rules. However, no such rule set exists for intracellular distribution. Kilgore et al …

[HTML][HTML] Mapping the energy landscape of PROTAC-mediated protein-protein interactions

JA Villegas, TM Vaid, ME Johnson… - Computational and …, 2023 - Elsevier
A principal challenge in computational modeling of macromolecules is the vast
conformational space that arises out of large numbers of atomic degrees of freedom …

Mapping interactions between disordered regions reveals promiscuity in biomolecular condensate formation

A Gilat, B Dubrueil, ED Levy - bioRxiv, 2023 - biorxiv.org
Intrinsically-disordered regions (IDRs) promote intracellular phase separation and the
formation of biomolecular condensates through interactions encoded in their primary …

Confident protein datasets for liquid-liquid phase separation studies

C Pintado-Grima, O Bárcenas, V Iglesias… - 2024 - researchsquare.com
Background Proteins self-organize in dynamic cellular environments by assembling into
reversible biomolecular condensates through liquid-liquid phase separation (LLPS). These …

Navigating the Cellular Crowd: Physicochemical Properties of Protein Surfaces as Evolved Interaction Guides

E Vallina Estrada - 2023 - diva-portal.org
The cellular interior is characterised by high concentrations of macromolecules. Compared
with dilute conditions, the crowd modifies proteins' ability to fold, diffuse and, ultimately, carry …