Structural and hydrodynamic properties of an intrinsically disordered region of a germ cell-specific protein on phase separation
Jacob P. Brady,Patrick Farber,Ashok Sekhar,Yi-Hsuan Lin,Rui Huang,Alaji Bah,Timothy J. Nott,Hue Sun Chan,Andrew Baldwin,Julie D. Forman-Kay,Lewis E. Kay +10 more
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TLDR
Observation of a network of interchain interactions, as established by NOE spectroscopy, shows the importance of Phe and Arg interactions in driving the phase separation of Ddx4, while the salt dependence of both low- and high-concentration regions of phase diagrams establishes an important role for electrostatic interactions.Abstract:
Membrane encapsulation is frequently used by the cell to sequester biomolecules and compartmentalize their function. Cells also concentrate molecules into phase-separated protein or protein/nucleic acid "membraneless organelles" that regulate a host of biochemical processes. Here, we use solution NMR spectroscopy to study phase-separated droplets formed from the intrinsically disordered N-terminal 236 residues of the germ-granule protein Ddx4. We show that the protein within the concentrated phase of phase-separated Ddx4, [Formula: see text], diffuses as a particle of 600-nm hydrodynamic radius dissolved in water. However, NMR spectra reveal sharp resonances with chemical shifts showing [Formula: see text] to be intrinsically disordered. Spin relaxation measurements indicate that the backbone amides of [Formula: see text] have significant mobility, explaining why high-resolution spectra are observed, but motion is reduced compared with an equivalently concentrated nonphase-separating control. Observation of a network of interchain interactions, as established by NOE spectroscopy, shows the importance of Phe and Arg interactions in driving the phase separation of Ddx4, while the salt dependence of both low- and high-concentration regions of phase diagrams establishes an important role for electrostatic interactions. The diffusion of a series of small probes and the compact but disordered 4E binding protein 2 (4E-BP2) protein in [Formula: see text] are explained by an excluded volume effect, similar to that found for globular protein solvents. No changes in structural propensities of 4E-BP2 dissolved in [Formula: see text] are observed, while changes to DNA and RNA molecules have been reported, highlighting the diverse roles that proteinaceous solvents play in dictating the properties of dissolved solutes.read more
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Coactivator condensation at super-enhancers links phase separation and gene control
Benjamin R. Sabari,Alessandra Dall’Agnese,Ann Boija,Isaac A. Klein,Isaac A. Klein,Eliot L. Coffey,Krishna Shrinivas,Brian J. Abraham,Nancy M. Hannett,Alicia V. Zamudio,John C. Manteiga,Charles H. Li,Yang Eric Guo,Daniel S. Day,Jurian Schuijers,Eliza Vasile,Sohail Malik,Denes Hnisz,Tong Ihn Lee,Ibrahim I Cisse,Robert G. Roeder,Phillip A. Sharp,Arup K. Chakraborty,Richard A. Young +23 more
TL;DR: It is postulated that super-enhancers are phase-separated multimolecular assemblies, also known as biomolecular condensates, which provide a means to compartmentalize and concentrate biochemical reactions within cells.
Journal ArticleDOI
Protein Phase Separation: A New Phase in Cell Biology.
Steven Boeynaems,Steven Boeynaems,Simon Alberti,Nicolas L. Fawzi,Tanja Mittag,Magdalini Polymenidou,Frederic Rousseau,Frederic Rousseau,Joost Schymkowitz,Joost Schymkowitz,James Shorter,Benjamin Wolozin,Ludo Van Den Bosch,Peter Tompa,Peter Tompa,Monika Fuxreiter +15 more
TL;DR: A combination of techniques from cell biology, biophysics, physical chemistry, structural biology, and bioinformatics are starting to help establish the molecular principles of an emerging field, thus paving the way for exciting discoveries, including novel therapeutic approaches for the treatment of age-related disorders.
Journal ArticleDOI
A Molecular Grammar Governing the Driving Forces for Phase Separation of Prion-like RNA Binding Proteins
Jie Wang,Jeong-Mo Choi,Alex S. Holehouse,Hyun O. Lee,Xiaojie Zhang,Marcus Jahnel,Shovamayee Maharana,Regis P. Lemaitre,Andrei Pozniakovsky,David N. Drechsel,Ina Poser,Rohit V. Pappu,Simon Alberti,Anthony A. Hyman +13 more
TL;DR: A model is developed to show that the measured saturation concentrations of phase separation are inversely proportional to the product of the numbers of arginine and tyrosine residues, which suggests it is possible to predict phase-separation properties based on amino acid sequences.
Journal ArticleDOI
Valence and patterning of aromatic residues determine the phase behavior of prion-like domains
Erik W. Martin,Alex S. Holehouse,Ivan Peran,Mina Farag,J. Jeremías Incicco,Anne Bremer,Christy R. Grace,Andrea Soranno,Rohit V. Pappu,Tanja Mittag +9 more
TL;DR: It is shown that the numbers (valence) of aromatic residues in PLDs determine the extent of temperature-dependent compaction of individual molecules in dilute solutions, which determines full binodals that quantify concentrations of PLDs within coexisting dilute and dense phases as a function of temperature.
Journal ArticleDOI
Pi-Pi contacts are an overlooked protein feature relevant to phase separation.
Robert M. Vernon,Paul Andrew Chong,Brian Tsang,Tae Hun Kim,Alaji Bah,Patrick Farber,Hong Lin,Julie D. Forman-Kay +7 more
TL;DR: It is found that pi-pi interactions involving non-aromatic groups are widespread, underestimated by force-fields used in structure calculations and correlated with solvation and lack of regular secondary structure, properties associated with disordered regions.
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