Phase separation of FG-nucleoporins in nuclear pore complexes

Biomolecular condensates and cancer

(2021) Ann Boija et al.   CANCER CELL

Recent Developments in the Field of Intrinsically Disordered Proteins: Intrinsic Disorder–Based Emergence in Cellular Biology in Light of the Physiological and Pathological Liquid–Liquid Phase Transitions

(2021) Vladimir N. Uversky   Annual Review of Biophysics

Prevalence and functionality of intrinsic disorder in human FG-nucleoporins

(2021) Denzelle Lee Lyngdoh et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

DisoLipPred: accurate prediction of disordered lipid-binding residues in protein sequences with deep recurrent networks and transfer learning

(2021) Akila Katuwawala et al.   BIOINFORMATICS

FG nucleoporins feature unique patterns that distinguish them from other IDPs

(2021) Mohaddeseh Peyro et al.   BIOPHYSICAL JOURNAL

Prevalence and species distribution of the low-complexity, amyloid-like, reversible, kinked segment (LARKS) structural motif in amyloid-like fibrils

(2021) Michael P. Hughes et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A proximity-dependent biotinylation map of a human cell

(2021) Christopher D. Go et al.   NATURE

Emerging Roles of Liquid–Liquid Phase Separation in Cancer: From Protein Aggregation to Immune-Associated Signaling

(2021) Jiahua Lu et al.   Frontiers in Cell and Developmental Biology

α-Synuclein aggregation nucleates through liquid–liquid phase separation

(2020) Soumik Ray et al.   Nature Chemistry

Nuclear Periphery Takes Center Stage: The Role of Nuclear Pore Complexes in Cell Identity and Aging

(2020) Ukrae H. Cho et al.   NEURON

Phase Separation and Neurodegenerative Diseases: A Disturbance in the Force

(2020) Aurélie Zbinden et al.   DEVELOPMENTAL CELL

Tunable multiphase dynamics of arginine and lysine liquid condensates

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

ODiNPred: comprehensive prediction of protein order and disorder

(2020) Rupashree Dass et al.   Scientific Reports

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

Stoichiometry controls activity of phase-separated clusters of actin signaling proteins

(2019) Lindsay B. Case et al.   SCIENCE

Altered Nup153 Expression Impairs the Function of Cultured Hippocampal Neural Stem Cells Isolated from a Mouse Model of Alzheimer’s Disease

(2019) Lucia Leone et al.   MOLECULAR NEUROBIOLOGY

Matter over mind: Liquid phase separation and neurodegeneration

(2019) Shana Elbaum-Garfinkle   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2019) Simon Alberti et al.   CELL

Phase separation of 53 BP 1 determines liquid‐like behavior of DNA repair compartments

(2019) Sinan Kilic et al.   EMBO JOURNAL

Molecular interactions underlying liquid−liquid phase separation of the FUS low-complexity domain

(2019) Anastasia C. Murthy et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structural basis for reversible amyloids of hnRNPA1 elucidates their role in stress granule assembly

(2019) Xinrui Gui et al.   Nature Communications

Liquid–Liquid Phase Separation in Disease

(2019) Simon Alberti et al.   Annual Review of Genetics

LLPSDB: a database of proteins undergoing liquid–liquid phase separation in vitro

(2019) Qian Li et al.   NUCLEIC ACIDS RESEARCH

Nuclear Pores Assemble from Nucleoporin Condensates During Oogenesis

(2019) Bernhard Hampoelz et al.   CELL

Organization of Chromatin by Intrinsic and Regulated Phase Separation

(2019) Bryan A. Gibson et al.   CELL

Oncogenic potential of nucleoporins in non-hematological cancers: recent update beyond chromosome translocation and gene fusion

(2019) Adhiraj Roy et al.   JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY

Properties of Stress Granule and P-Body Proteomes

(2019) Ji-Young Youn et al.   MOLECULAR CELL

PhaSepDB: a database of liquid–liquid phase separation related proteins

(2019) Kaiqiang You et al.   NUCLEIC ACIDS RESEARCH

Modulation of actin polymerization affects nucleocytoplasmic transport in multiple forms of amyotrophic lateral sclerosis

(2019) Anthony Giampetruzzi et al.   Nature Communications

In Aqua Veritas: The Indispensable yet Mostly Ignored Role of Water in Phase Separation and Membrane-less Organelles

(2018) Boris Y. Zaslavsky et al.   BIOCHEMISTRY

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

(2018) Jie Wang et al.   CELL

Tau protein liquid–liquid phase separation can initiate tau aggregation

(2018) Susanne Wegmann et al.   EMBO JOURNAL

Thermodynamic characterization of the multivalent interactions underlying rapid and selective translocation through the nuclear pore complex

(2018) Ryo Hayama et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Advances in Understanding Stimulus-Responsive Phase Behavior of Intrinsically Disordered Protein Polymers

(2018) Kiersten M. Ruff et al.   JOURNAL OF MOLECULAR BIOLOGY

Aggregation, Phase Separation and Spatial Morphologies of the Assemblies of FG Nucleoporins

(2018) Anton Zilman   JOURNAL OF MOLECULAR BIOLOGY

What lava lamps and vinaigrette can teach us about cell biology

(2018) Elie Dolgin   NATURE

Developing a molecular dynamics force field for both folded and disordered protein states

(2018) Paul Robustelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA buffers the phase separation behavior of prion-like RNA binding proteins

(2018) Shovamayee Maharana et al.   SCIENCE

A liquid phase of synapsin and lipid vesicles

(2018) Dragomir Milovanovic et al.   SCIENCE

Phase separation of a yeast prion protein promotes cellular fitness

(2018) Titus M. Franzmann et al.   SCIENCE

Protein Phase Separation: A New Phase in Cell Biology

(2018) Steven Boeynaems et al.   TRENDS IN CELL BIOLOGY

mTOR Regulates Phase Separation of PGL Granules to Modulate Their Autophagic Degradation

(2018) Gangming Zhang et al.   CELL

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

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

RNA polymerase II clustering through carboxy-terminal domain phase separation

(2018) Marc Boehning et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Tau Protein Disrupts Nucleocytoplasmic Transport in Alzheimer’s Disease

(2018) Bahareh Eftekharzadeh et al.   NEURON

Phospho-Tau Impairs Nuclear-Cytoplasmic Transport

(2018) Timir Tripathi et al.   ACS Chemical Neuroscience

Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome

(2018) Yongdae Shin et al.   CELL

Nuclear condensates of the Polycomb protein chromobox 2 (CBX2) assemble through phase separation

(2018) Roubina Tatavosian et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Karyopherins regulate nuclear pore complex barrier and transport function

(2017) Larisa E. Kapinos et al.   JOURNAL OF CELL BIOLOGY

Programming molecular self-assembly of intrinsically disordered proteins containing sequences of low complexity

(2017) Joseph R. Simon et al.   Nature Chemistry

Biomolecular condensates: organizers of cellular biochemistry

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

Polyglutamine-Expanded Huntingtin Exacerbates Age-Related Disruption of Nuclear Integrity and Nucleocytoplasmic Transport

(2017) Fatima Gasset-Rosa et al.   NEURON

TIA1 Mutations in Amyotrophic Lateral Sclerosis and Frontotemporal Dementia Promote Phase Separation and Alter Stress Granule Dynamics

(2017) Ian R. Mackenzie et al.   NEURON

Mutant Huntingtin Disrupts the Nuclear Pore Complex

(2017) Jonathan C. Grima et al.   NEURON

Amyotrophic lateral sclerosis-linked mutations increase the viscosity of liquid-like TDP-43 RNP granules in neurons

(2017) Pallavi P. Gopal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural and hydrodynamic properties of an intrinsically disordered region of a germ cell-specific protein on phase separation

(2017) Jacob P. Brady et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Liquid phase condensation in cell physiology and disease

(2017) Yongdae Shin et al.   SCIENCE

Simple rules for passive diffusion through the nuclear pore complex

(2016) Benjamin L. Timney et al.   JOURNAL OF CELL BIOLOGY

The Multiple Faces of Disordered Nucleoporins

(2016) Edward A. Lemke   JOURNAL OF MOLECULAR BIOLOGY

Sequence Determinants of Intracellular Phase Separation by Complex Coacervation of a Disordered Protein

(2016) Chi W. Pak et al.   MOLECULAR CELL

Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex

(2016) Barak Raveh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Architecture of the symmetric core of the nuclear pore

(2016) D. H. Lin et al.   SCIENCE

Molecular architecture of the inner ring scaffold of the human nuclear pore complex

(2016) J. Kosinski et al.   SCIENCE

Phase separation of signaling molecules promotes T cell receptor signal transduction

(2016) Xiaolei Su et al.   SCIENCE

ALS Mutations Disrupt Phase Separation Mediated by α-Helical Structure in the TDP-43 Low-Complexity C-Terminal Domain

(2016) Alexander E. Conicella et al.   STRUCTURE

Transport Selectivity of Nuclear Pores, Phase Separation, and Membraneless Organelles

(2016) H. Broder Schmidt et al.   TRENDS IN BIOCHEMICAL SCIENCES

A Concentration-Dependent Liquid Phase Separation Can Cause Toxicity upon Increased Protein Expression

(2016) Benedetta Bolognesi et al.   Cell Reports

A pH-driven transition of the cytoplasm from a fluid- to a solid-like state promotes entry into dormancy

(2016) Matthias Christoph Munder et al.   eLife

A physical model describing the interaction of nuclear transport receptors with FG nucleoporin domain assemblies

(2016) Raphael Zahn et al.   eLife

Simple biophysics underpins collective conformations of the intrinsically disordered proteins of the Nuclear Pore Complex

(2016) Andrei Vovk et al.   eLife

Spatial patterning of P granules by RNA-induced phase separation of the intrinsically-disordered protein MEG-3

(2016) Jarrett Smith et al.   eLife

CIDER: Classification of Intrinsically Disordered Ensemble Regions

(2015) Alex S. Holehouse et al.   BIOPHYSICAL JOURNAL

Promiscuous Binding of Karyopherin β 1 Modulates FG Nucleoporin Barrier Function and Expedites NTF2 Transport Kinetics

(2015) Raphael S. Wagner et al.   BIOPHYSICAL JOURNAL

Plasticity of an Ultrafast Interaction between Nucleoporins and Nuclear Transport Receptors

(2015) Sigrid Milles et al.   CELL

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

(2015) Amandine Molliex et al.   CELL

A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation

(2015) Avinash Patel et al.   CELL

Phase Transition of Spindle-Associated Protein Regulate Spindle Apparatus Assembly

(2015) Hao Jiang et al.   CELL

Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States

(2015) Stefano Piana et al.   JOURNAL OF PHYSICAL CHEMISTRY B

RNA Controls PolyQ Protein Phase Transitions

(2015) Huaiying Zhang et al.   MOLECULAR CELL

Formation and Maturation of Phase-Separated Liquid Droplets by RNA-Binding Proteins

(2015) Yuan Lin et al.   MOLECULAR CELL

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

Phosphorylation-mediated RNA/peptide complex coacervation as a model for intracellular liquid organelles

(2015) William M. Aumiller et al.   Nature Chemistry

Encoding phase transitions

(2015) Alex S. Holehouse et al.   NATURE MATERIALS

Cytoplasmic protein aggregates interfere with nucleocytoplasmic transport of protein and RNA

(2015) A. C. Woerner et al.   SCIENCE

Post-translationalO-GlcNAcylation is essential for nuclear pore integrity and maintenance of the pore selectivity filter

(2015) Yanping Zhu et al.   Journal of Molecular Cell Biology

Evolutionarily Conserved Sequence Features Regulate the Formation of the FG Network at the Center of the Nuclear Pore Complex

(2015) M. Peyro et al.   Scientific Reports

Importin-β modulates the permeability of the nuclear pore complex in a Ran-dependent manner

(2015) Alan R Lowe et al.   eLife

Nup98 FG domains from diverse species spontaneously phase-separate into particles with nuclear pore-like permselectivity

(2015) Hermann Broder Schmidt et al.   eLife

Nucleoporin's Like Charge Regions Are Major Regulators of FG Coverage and Dynamics Inside the Nuclear Pore Complex

(2015) Mohaddeseh Peyro et al.   PLoS One

Intrinsically Disordered Proteins and Intrinsically Disordered Protein Regions

(2014) Christopher J. Oldfield et al.   Annual Review of Biochemistry

PLAAC: a web and command-line application to identify proteins with prion-like amino acid composition

(2014) A. K. Lancaster et al.   BIOINFORMATICS

Karyopherin-Centric Control of Nuclear Pores Based on Molecular Occupancy and Kinetic Analysis of Multivalent Binding with FG Nucleoporins

(2014) Larisa E. Kapinos et al.   BIOPHYSICAL JOURNAL

Nuclear Pore Complex Protein Sequences Determine Overall Copolymer Brush Structure and Function

(2014) David Ando et al.   BIOPHYSICAL JOURNAL

Exploring Free-Energy Landscapes of Intrinsically Disordered Proteins at Atomic Resolution Using NMR Spectroscopy

(2014) Malene Ringkjøbing Jensen et al.   CHEMICAL REVIEWS

Classification of Intrinsically Disordered Regions and Proteins

(2014) Robin van der Lee et al.   CHEMICAL REVIEWS

Intrinsically disordered proteins as crucial constituents of cellular aqueous two phase systems and coacervates

(2014) Vladimir N. Uversky et al.   FEBS LETTERS

Role of Molecular Charge in Nucleocytoplasmic Transport

(2014) Alexander Goryaynov et al.   PLoS One

Cohesiveness tunes assembly and morphology of FG nucleoporin domain meshworks – Implications for nuclear pore permeability

(2013) Nico B. Eisele et al.   BIOPHYSICAL JOURNAL

Integrated Structural Analysis of the Human Nuclear Pore Complex Scaffold

(2013) Khanh Huy Bui et al.   CELL

Physical Motif Clustering within Intrinsically Disordered Nucleoporin Sequences Reveals Universal Functional Features

(2013) David Ando et al.   PLoS One

Differential scanning calorimetry as a tool for protein folding and stability

(2012) Christopher M. Johnson   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins

(2012) Lukasz P Kozlowski et al.   BMC BIOINFORMATICS

The tip of the iceberg: RNA-binding proteins with prion-like domains in neurodegenerative disease

(2012) Oliver D. King et al.   BRAIN RESEARCH

The Permeability of Reconstituted Nuclear Pores Provides Direct Evidence for the Selective Phase Model

(2012) Bastian B. Hülsmann et al.   CELL

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

(2012) Masato Kato et al.   CELL

Ranbp2 haploinsufficiency mediates distinct cellular and biochemical phenotypes in brain and retinal dopaminergic and glia cells elicited by the Parkinsonian neurotoxin, 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)

(2012) Kyoung-in Cho et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Systematic analysis of barrier-forming FG hydrogels from Xenopus nuclear pore complexes

(2012) Aksana A Labokha et al.   EMBO JOURNAL

Facilitated aggregation of FG nucleoporins under molecular crowding conditions

(2012) Sigrid Milles et al.   EMBO REPORTS

Phase transitions in the assembly of multivalent signalling proteins

(2012) Pilong Li et al.   NATURE

D2P2: database of disordered protein predictions

(2012) Matt E. Oates et al.   NUCLEIC ACIDS RESEARCH

The Human Nuclear Pore Complex as Revealed by Cryo-Electron Tomography

(2012) Tal Maimon et al.   STRUCTURE

ESpritz: accurate and fast prediction of protein disorder

(2011) Ian Walsh et al.   BIOINFORMATICS

Single Molecule Study of the Intrinsically Disordered FG-Repeat Nucleoporin 153

(2011) Sigrid Milles et al.   BIOPHYSICAL JOURNAL

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Uncertainty analysis in protein disorder prediction

(2011) Mohamed F. Ghalwash et al.   Molecular BioSystems

Simulations of nuclear pore transport yield mechanistic insights and quantitative predictions

(2011) J. S. Mincer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Brownian Dynamics Simulation of Nucleocytoplasmic Transport: A Coarse-Grained Model for the Functional State of the Nuclear Pore Complex

(2011) Ruhollah Moussavi-Baygi et al.   PLoS Computational Biology

The C. elegans homolog of nucleoporin Nup98 is required for the integrity and function of germline P granules

(2010) E. Voronina et al.   DEVELOPMENT

Mutant FUS proteins that cause amyotrophic lateral sclerosis incorporate into stress granules

(2010) Daryl A. Bosco et al.   HUMAN MOLECULAR GENETICS

Induction of Amyloid Fibrils by the C-Terminal Fragments of TDP-43 in Amyotrophic Lateral Sclerosis

(2010) Allan K.-H. Chen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A Bimodal Distribution of Two Distinct Categories of Intrinsically Disordered Structures with Separate Functions in FG Nucleoporins

(2010) Justin Yamada et al.   MOLECULAR & CELLULAR PROTEOMICS

TDP-43 Is Directed to Stress Granules by Sorbitol, a Novel Physiological Osmotic and Oxidative Stressor

(2010) C. M. Dewey et al.   MOLECULAR AND CELLULAR BIOLOGY

Amyloid-like interactions within nucleoporin FG hydrogels

(2010) C. Ader et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PreDisorder: ab initio sequence-based prediction of protein disordered regions

(2009) Xin Deng et al.   BMC BIOINFORMATICS

FG/FxFG as well as GLFG repeats form a selective permeability barrier with self-healing properties

(2009) Steffen Frey et al.   EMBO JOURNAL

Structural Analysis of a Metazoan Nuclear Pore Complex Reveals a Fused Concentric Ring Architecture

(2009) Daphna Frenkiel-Krispin et al.   JOURNAL OF MOLECULAR BIOLOGY

Transport-Related Structures and Processes of the Nuclear Pore Complex Studied through Molecular Dynamics

(2009) Lingling Miao et al.   STRUCTURE

Intrinsic disorder prediction from the analysis of multiple protein fold recognition models

(2008) Liam J. McGuffin   BIOINFORMATICS

A role for Q/N-rich aggregation-prone regions in P-body localization

(2008) M. A. M. Reijns et al.   JOURNAL OF CELL SCIENCE

TOP-IDP-Scale: A New Amino Acid Scale Measuring Propensity for Intrinsic Disorder

(2008) Andrew Campen et al.   PROTEIN AND PEPTIDE LETTERS