Valency and Binding Affinity Variations Can Regulate the Multilayered Organization of Protein Condensates with Many Components

Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions

(2021) Georg Krainer et al.   Nature Communications

Multidimensional Phase Diagrams for Multicomponent Systems Comprising Multivalent Proteins

(2020) Furqan Dar et al.   BIOPHYSICAL JOURNAL

Model for disordered proteins with strongly sequence-dependent liquid phase behavior

(2020) Antonia Statt et al.   JOURNAL OF CHEMICAL PHYSICS

Multiphase Complex Coacervate Droplets

(2020) Tiemei Lu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Valence and patterning of aromatic residues determine the phase behavior of prion-like domains

(2020) Erik W. Martin et al.   SCIENCE

Phase separation provides a mechanism to reduce noise in cells

(2020) A. Klosin et al.   SCIENCE

Competing Protein-RNA Interaction Networks Control Multiphase Intracellular Organization

(2020) David W. Sanders et al.   CELL

RNA-Induced Conformational Switching and Clustering of G3BP Drive Stress Granule Assembly by Condensation

(2020) Jordina Guillén-Boixet et al.   CELL

Single-Protein Collapse Determines Phase Equilibria of a Biological Condensate

(2020) Han-Yi Chou et al.   Journal of Physical Chemistry Letters

Liquid network connectivity regulates the stability and composition of biomolecular condensates with many components

(2020) Jorge R. Espinosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

α-Synuclein aggregation nucleates through liquid–liquid phase separation

(2020) Soumik Ray et al.   Nature Chemistry

RNA contributions to the form and function of biomolecular condensates

(2020) Christine Roden et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Phase separation of Arabidopsis EMB1579 controls transcription, mRNA splicing, and development

(2020) Yiling Zhang et al.   PLOS BIOLOGY

Unraveling Molecular Interactions in Liquid–Liquid Phase Separation of Disordered Proteins by Atomistic Simulations

(2020) Matteo Paloni et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Expansion of Intrinsically Disordered Proteins Increases the Range of Stability of Liquid–Liquid Phase Separation

(2020) Adiran Garaizar et al.   MOLECULES

Tunable multiphase dynamics of arginine and lysine liquid condensates

(2020) Rachel S. Fisher et al.   Nature Communications

Simulation of FUS Protein Condensates with an Adapted Coarse-Grained Model

(2020) Zakarya Benayad et al.   Journal of Chemical Theory and Computation

Molecular Details of Protein Condensates Probed by Microsecond Long Atomistic Simulations

(2020) Wenwei Zheng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Considerations and Challenges in Studying Liquid-Liquid Phase Separation and Biomolecular Condensates

(2019) Simon Alberti et al.   CELL

Spontaneous driving forces give rise to protein−RNA condensates with coexisting phases and complex material properties

(2019) Steven Boeynaems et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simulation methods for liquid–liquid phase separation of disordered proteins

(2019) Gregory L Dignon et al.   Current Opinion in Chemical Engineering

Breakdown of the law of rectilinear diameter and related surprises in the liquid-vapor coexistence in systems of patchy particles

(2019) Jorge R. Espinosa et al.   JOURNAL OF CHEMICAL PHYSICS

RNA recognition motifs of disease-linked RNA-binding proteins contribute to amyloid formation

(2019) Sashank Agrawal et al.   Scientific Reports

Formation of Multiphase Complex Coacervates and Partitioning of Biomolecules within them

(2019) Gregory A. Mountain et al.   BIOMACROMOLECULES

The liquid nucleome – phase transitions in the nucleus at a glance

(2019) Amy R. Strom et al.   JOURNAL OF CELL SCIENCE

LASSI: A lattice model for simulating phase transitions of multivalent proteins

(2019) Jeong-Mo Choi et al.   PLoS Computational Biology

TDP-43 and FUS–structural insights into RNA recognition and self-association

(2019) Fionna E Loughlin et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Theories for Sequence-Dependent Phase Behaviors of Biomolecular Condensates

(2018) Yi-Hsuan Lin et al.   BIOCHEMISTRY

Phase Transitions in the Assembly and Function of Human miRISC

(2018) Jessica Sheu-Gruttadauria et al.   CELL

A Molecular Grammar Governing the Driving Forces for Phase Separation of Prion-like RNA Binding Proteins

(2018) Jie Wang et al.   CELL

Prion-like low-complexity sequences: Key regulators of protein solubility and phase behavior

(2018) Titus Franzmann et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Quality Control of Membraneless Organelles

(2018) Simon Alberti et al.   JOURNAL OF MOLECULAR BIOLOGY

Controlling compartmentalization by non-membrane-bound organelles

(2018) Richard J. Wheeler et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The RNA face of phase separation

(2018) Magdalini Polymenidou   SCIENCE

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

Self-interaction of NPM1 modulates multiple mechanisms of liquid–liquid phase separation

(2018) Diana M. Mitrea et al.   Nature Communications

Liquid-Liquid Phase Separation of Patchy Particles Illuminates Diverse Effects of Regulatory Components on Protein Droplet Formation

(2018) Valery Nguemaha et al.   Scientific Reports

Different Material States of Pub1 Condensates Define Distinct Modes of Stress Adaptation and Recovery

(2018) Sonja Kroschwald et al.   Cell Reports

Sequence determinants of protein phase behavior from a coarse-grained model

(2018) Gregory L. Dignon et al.   PLoS Computational Biology

Cancer Mutations of the Tumor Suppressor SPOP Disrupt the Formation of Active, Phase-Separated Compartments

(2018) Jill J. Bouchard et al.   MOLECULAR CELL

Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome

(2018) Yongdae Shin et al.   CELL

Advances in coarse-grained modeling of macromolecular complexes

(2018) Alexander J Pak et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Conformational preferences and phase behavior of intrinsically disordered low complexity sequences: insights from multiscale simulations

(2018) Kiersten M Ruff et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution

(2017) Jingyi Fei et al.   JOURNAL OF CELL SCIENCE

Biomolecular condensates: organizers of cellular biochemistry

(2017) Salman F. Banani et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Liquid phase condensation in cell physiology and disease

(2017) Yongdae Shin et al.   SCIENCE

Liquid–liquid phase separation of the microtubule-binding repeats of the Alzheimer-related protein Tau

(2017) Susmitha Ambadipudi et al.   Nature Communications

Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins

(2017) Tyler S Harmon et al.   eLife

Characterizing DNA Star-Tile-Based Nanostructures Using a Coarse-Grained Model

(2016) John S. Schreck et al.   ACS Nano

ATPase-Modulated Stress Granules Contain a Diverse Proteome and Substructure

(2016) Saumya Jain et al.   CELL

C9orf72 Dipeptide Repeats Impair the Assembly, Dynamics, and Function of Membrane-Less Organelles

(2016) Kyung-Ha Lee et al.   CELL

Compositional Control of Phase-Separated Cellular Bodies

(2016) Salman F. Banani et al.   CELL

Coexisting Liquid Phases Underlie Nucleolar Subcompartments

(2016) Marina Feric et al.   CELL

Seeding approach to crystal nucleation

(2016) Jorge R. Espinosa et al.   JOURNAL OF CHEMICAL PHYSICS

Phase separation of signaling molecules promotes T cell receptor signal transduction

(2016) Xiaolei Su et al.   SCIENCE

Nucleophosmin integrates within the nucleolus via multi-modal interactions with proteins displaying R-rich linear motifs and rRNA

(2016) Diana M Mitrea et al.   eLife

The Size of the Human Proteome: The Width and Depth

(2016) Elena A. Ponomarenko et al.   International Journal of Analytical Chemistry

The LC Domain of hnRNPA2 Adopts Similar Conformations in Hydrogel Polymers, Liquid-like Droplets, and Nuclei

(2015) Siheng Xiang et al.   CELL

Phase Separation by Low Complexity Domains Promotes Stress Granule Assembly and Drives Pathological Fibrillization

(2015) Amandine Molliex et al.   CELL

CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences

(2015) Kiersten M. Ruff et al.   JOURNAL OF CHEMICAL PHYSICS

Residue-by-Residue View of In Vitro FUS Granules that Bind the C-Terminal Domain of RNA Polymerase II

(2015) Kathleen A. Burke et al.   MOLECULAR CELL

Phase Transition of a Disordered Nuage Protein Generates Environmentally Responsive Membraneless Organelles

(2015) Timothy J. Nott et al.   MOLECULAR CELL

Polymer physics of intracellular phase transitions

(2015) Clifford P. Brangwynne et al.   Nature Physics

The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics

(2015) Shana Elbaum-Garfinkle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Liquid-Liquid Phase Separation in Biology

(2014) Anthony A. Hyman et al.   Annual Review of Cell and Developmental Biology

The mold integration method for the calculation of the crystal-fluid interfacial free energy from simulations

(2014) J. R. Espinosa et al.   JOURNAL OF CHEMICAL PHYSICS

On fluid-solid direct coexistence simulations: The pseudo-hard sphere model

(2013) Jorge R. Espinosa et al.   JOURNAL OF CHEMICAL PHYSICS

The changing scene of amyotrophic lateral sclerosis

(2013) Wim Robberecht et al.   NATURE REVIEWS NEUROSCIENCE

Coarse-graining DNA for simulations of DNA nanotechnology

(2013) Jonathan P. K. Doye et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Cell-free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers within Hydrogels

(2012) Masato Kato et al.   CELL

Pseudo hard-sphere potential for use in continuous molecular-dynamics simulation of spherical and chain molecules

(2012) J. Jover et al.   JOURNAL OF CHEMICAL PHYSICS

Phase transitions in the assembly of multivalent signalling proteins

(2012) Pilong Li et al.   NATURE

Parkinson's Disease: Genetics and Pathogenesis

(2011) Joshua M. Shulman et al.   Annual Review of Pathology-Mechanisms of Disease

MSI4/FVE interacts with CUL4-DDB1 and a PRC2-like complex to control epigenetic regulation of flowering time in Arabidopsis

(2011) M. Pazhouhandeh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prion-like transmission of protein aggregates in neurodegenerative diseases

(2010) Patrik Brundin et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Association of limited valence patchy particles in two dimensions

(2010) John Russo et al.   Soft Matter

Reversible gels of patchy particles: Role of the valence

(2009) John Russo et al.   JOURNAL OF CHEMICAL PHYSICS

Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool

(2009) Alexander Stukowski   MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING

Dynamics of component exchange at PML nuclear bodies

(2008) S. Weidtkamp-Peters et al.   JOURNAL OF CELL SCIENCE

Morphology and Phase Separation of Hydrophobic Clusters of Soy Globular Protein Polymers

(2007) Xiuzhi Susan Sun et al.   MACROMOLECULAR BIOSCIENCE