Protein folding and quinary interactions: creating cellular organisation through functional disorder

Life and Work of Stress Granules and Processing Bodies: New Insights into Their Formation and Function

(2018) Marcelo Perez-Pepe et al.   BIOCHEMISTRY

Surface Charge Modulates Protein–Protein Interactions in Physiologically Relevant Environments

(2018) Alex J. Guseman et al.   BIOCHEMISTRY

The physical forces mediating self-association and phase-separation in the C-terminal domain of TDP-43

(2018) Hao-Ru Li et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Non-steric Interactions Predict the Trend and Steric Interactions the Offset of Protein Stability in Cells

(2018) Caitlin M. Davis et al.   CHEMPHYSCHEM

How does solvation in the cell affect protein folding and binding?

(2018) Caitlin M Davis et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Pressure- and heat-induced protein unfolding in bacterial cells: crowding vs . sticking

(2018) Timothy Chen et al.   FEBS LETTERS

Extant fold-switching proteins are widespread

(2018) Lauren L. Porter 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

Phase separation of a yeast prion protein promotes cellular fitness

(2018) Titus M. Franzmann et al.   SCIENCE

Why Do Disordered and Structured Proteins Behave Differently in Phase Separation?

(2018) Huan-Xiang Zhou et al.   TRENDS IN BIOCHEMICAL SCIENCES

Paraspeckles: Where Long Noncoding RNA Meets Phase Separation

(2018) Archa H. Fox et al.   TRENDS IN BIOCHEMICAL SCIENCES

Protein Phase Separation: A New Phase in Cell Biology

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

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

(2018) Valery Nguemaha et al.   Scientific Reports

Inherent flexibility of CLIC6 revealed by crystallographic and solution studies

(2018) Alisa Ferofontov et al.   Scientific Reports

Intrinsically Disordered Regions Can Contribute Promiscuous Interactions to RNP Granule Assembly

(2018) David S.W. Protter et al.   Cell Reports

Osmotic Shock Induced Protein Destabilization in Living Cells and Its Reversal by Glycine Betaine

(2017) Samantha S. Stadmiller et al.   JOURNAL OF MOLECULAR BIOLOGY

Cosolutes, Crowding, and Protein Folding Kinetics

(2017) Annelise H. Gorensek-Benitez et al.   JOURNAL OF PHYSICAL CHEMISTRY B

RNA phase transitions in repeat expansion disorders

(2017) Ankur Jain et al.   NATURE

Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin

(2017) Adam G. Larson et al.   NATURE

Biomolecular condensates: organizers of cellular biochemistry

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

The case for defined protein folding pathways

(2017) S. Walter Englander et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Physicochemical code for quinary protein interactions inEscherichia coli

(2017) Xin Mu 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

Quinary interactions with an unfolded state ensemble

(2017) Rachel D. Cohen et al.   PROTEIN SCIENCE

A cell is more than the sum of its (dilute) parts: A brief history of quinary structure

(2017) Rachel D. Cohen et al.   PROTEIN SCIENCE

Liquid phase condensation in cell physiology and disease

(2017) Yongdae Shin et al.   SCIENCE

There Is an Inclusion for That: Material Properties of Protein Granules Provide a Platform for Building Diverse Cellular Functions

(2017) Daniel Kaganovich   TRENDS IN BIOCHEMICAL SCIENCES

An optimized strategy to measure protein stability highlights differences between cold and hot unfolded states

(2017) Caterina Alfano et al.   Nature Communications

Glycolytic Enzymes Coalesce in G Bodies under Hypoxic Stress

(2017) Meiyan Jin et al.   Cell Reports

Globular Protein Folding In Vitro and In Vivo

(2016) Martin Gruebele et al.   Annual Review of Biophysics

Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics

(2016) Luciano A. Abriata et al.   BIOPHYSICAL JOURNAL

Mechanisms and Consequences of Macromolecular Phase Separation

(2016) Louis-Philippe Bergeron-Sandoval et al.   CELL

Coexisting Liquid Phases Underlie Nucleolar Subcompartments

(2016) Marina Feric et al.   CELL

Grasping the nature of the cell interior: fromPhysiological ChemistrytoChemical Biology

(2016) Ciara Kyne et al.   FEBS Journal

Subcellular modulation of protein VlsE stability and folding kinetics

(2016) Jonathan Tai et al.   FEBS LETTERS

Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods

(2016) Xing Du et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Electrostatic Contributions to Protein Quinary Structure

(2016) Rachel D. Cohen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

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

In-cell thermodynamics and a new role for protein surfaces

(2016) Austin E. Smith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The role of negative selection in protein evolution revealed through the energetics of the native state ensemble

(2016) Jordan Hoffmann et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Cajal body and the nucleolus: “In a relationship” or “It's complicated”?

(2016) Laura Trinkle-Mulcahy et al.   RNA Biology

Phase separation of signaling molecules promotes T cell receptor signal transduction

(2016) Xiaolei Su et al.   SCIENCE

Macromolecular Crowding In Vitro , In Vivo , and In Between

(2016) Germán Rivas et al.   TRENDS IN BIOCHEMICAL SCIENCES

Structural Maturation of HIV-1 Reverse Transcriptase—A Metamorphic Solution to Genomic Instability

(2016) Robert London   Viruses-Basel

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 glucose-starvation response regulates the diffusion of macromolecules

(2016) Ryan P Joyner et al.   eLife

CPEB4 is regulated during cell cycle by ERK2/Cdk1-mediated phosphorylation and its assembly into liquid-like droplets

(2016) Jordina Guillén-Boixet et al.   eLife

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

Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm

(2016) Isseki Yu et al.   eLife

Probing Protein Quinary Interactions by In-Cell Nuclear Magnetic Resonance Spectroscopy

(2015) Subhabrata Majumder et al.   BIOCHEMISTRY

Reversible, Specific, Active Aggregates of Endogenous Proteins Assemble upon Heat Stress

(2015) Edward W.J. Wallace et al.   CELL

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

(2015) Amandine Molliex et al.   CELL

Transient Interactions of a Cytosolic Protein with Macromolecular and Vesicular Cosolutes: Unspecific and Specific Effects

(2015) Alberto Ceccon et al.   CHEMBIOCHEM

Revisiting a dogma: the effect of volume exclusion in molecular crowding

(2015) Anastasia Politou et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Functional roles of transiently and intrinsically disordered regions within proteins

(2015) Vladimir N. Uversky   FEBS Journal

Systemic control of protein synthesis through sequestration of translation and ribosome biogenesis factors during severe heat stress

(2015) Valeria Cherkasov et al.   FEBS LETTERS

Protein–Protein Interactions Affect Alpha Helix Stability in Crowded Environments

(2015) Bryanne Macdonald et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Polymer physics of intracellular phase transitions

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

Thermodynamics of protein destabilization in live cells

(2015) Jens Danielsson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quinary structure modulates protein stability in cells

(2015) William B. Monteith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Intracellular pH modulates quinary structure

(2015) Rachel D. Cohen et al.   PROTEIN SCIENCE

Design of protein switches based on an ensemble model of allostery

(2015) Jay H. Choi et al.   Nature Communications

Thermal fluctuations of immature SOD1 lead to separate folding and misfolding pathways

(2015) Ashok Sekhar et al.   eLife

Protein Crowder Charge and Protein Stability

(2014) Mohona Sarkar et al.   BIOCHEMISTRY

Conditionally and Transiently Disordered Proteins: Awakening Cryptic Disorder To Regulate Protein Function

(2014) Ursula Jakob 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

Amyloid Formation by Human Carboxypeptidase D Transthyretin-like Domain under Physiological Conditions

(2014) Javier Garcia-Pardo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Protein Folding Dynamics in the Cell

(2014) Irisbel Guzman et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protein Stabilization by Macromolecular Crowding through Enthalpy Rather Than Entropy

(2014) Michael Senske et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Challenges and dreams: physics of weak interactions essential to life

(2014) Peter Chien et al.   MOLECULAR BIOLOGY OF THE CELL

The ensemble nature of allostery

(2014) Hesam N. Motlagh et al.   NATURE

The amyloid state and its association with protein misfolding diseases

(2014) Tuomas P. J. Knowles et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Residue level quantification of protein stability in living cells

(2014) W. B. Monteith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phase transitions of multivalent proteins can promote clustering of membrane receptors

(2014) Sudeep Banjade et al.   eLife

Quinary protein structure and the consequences of crowding in living cells: Leaving the test-tube behind

(2013) Anna Jean Wirth et al.   BIOESSAYS

Direct Observation of Protein Unfolded State Compaction in the Presence of Macromolecular Crowding

(2013) Therese Mikaelsson et al.   BIOPHYSICAL JOURNAL

Regulated unfolding of proteins in signaling

(2013) Diana M. Mitrea et al.   FEBS LETTERS

The Extracellular Protein VlsE Is Destabilized Inside Cells

(2013) Irisbel Guzman et al.   JOURNAL OF MOLECULAR BIOLOGY

Deciphering Protein Stability in Cells

(2013) Anne Gershenson   JOURNAL OF MOLECULAR BIOLOGY

Unified Description of Urea Denaturation: Backbone and Side Chains Contribute Equally in the Transfer Model

(2013) Beate Moeser et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Reduced Native State Stability in Crowded Cellular Environment Due to Protein–Protein Interactions

(2013) Ryuhei Harada et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers

(2013) A. Sekhar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Impact of reconstituted cytosol on protein stability

(2013) M. Sarkar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The emergence of protein complexes: quaternary structure, dynamics and allostery

(2012) Tina Perica et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

An α Helix to β Barrel Domain Switch Transforms the Transcription Factor RfaH into a Translation Factor

(2012) Björn M. Burmann et al.   CELL

Macromolecular Crowding and Protein Stability

(2012) Yaqiang Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Temperature dependence of protein folding kinetics in living cells

(2012) M. Guo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Protein-Folding Problem, 50 Years On

(2012) K. A. Dill et al.   SCIENCE

Exploring Weak, Transient Protein–Protein Interactions in Crowded In Vivo Environments by In-Cell Nuclear Magnetic Resonance Spectroscopy

(2011) Qinghua Wang et al.   BIOCHEMISTRY

Native-State Interconversion of a Metamorphic Protein Requires Global Unfolding

(2011) Robert C. Tyler et al.   BIOCHEMISTRY

Protein Stability and Folding Kinetics in the Nucleus and Endoplasmic Reticulum of Eucaryotic Cells

(2011) A. Dhar et al.   BIOPHYSICAL JOURNAL

The two faces of Janus: functional interactions and protein aggregation

(2011) Annalisa Pastore et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Protein Folding Landscapes in the Living Cell

(2011) Simon Ebbinghaus et al.   Journal of Physical Chemistry Letters

Protein Crowding Tunes Protein Stability

(2011) Andrew C. Miklos et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Protein binding specificity versus promiscuity

(2010) Gideon Schreiber et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Macromolecular Crowding Remodels the Energy Landscape of a Protein by Favoring a More Compact Unfolded State

(2010) Jiang Hong et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Phase behavior of mixtures of human lens proteins Gamma D and Beta B1

(2010) Y. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure, function, and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding

(2010) Apratim Dhar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm

(2010) Sean R. McGuffee et al.   PLoS Computational Biology

Post-reductionist protein science, or putting Humpty Dumpty back together again

(2009) Lila M Gierasch et al.   Nature Chemical Biology

The induction of folding cooperativity by ligand binding drives the allosteric response of tetracycline repressor

(2009) Sean E. Reichheld et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins

(2009) T. P. Schrank et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Mad2 partial unfolding model: regulating mitosis through Mad2 conformational switching

(2008) John J. Skinner et al.   JOURNAL OF CELL BIOLOGY

Amyloid formation by globular proteins under native conditions

(2008) Fabrizio Chiti et al.   Nature Chemical Biology

Interconversion between two unrelated protein folds in the lymphotactin native state

(2008) Robbyn L. Tuinstra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BIOCHEMISTRY: Metamorphic Proteins

(2008) A. G. Murzin   SCIENCE

Protein Phase Behavior in Aqueous Solutions: Crystallization, Liquid-Liquid Phase Separation, Gels, and Aggregates

(2007) André C. Dumetz et al.   BIOPHYSICAL JOURNAL