Interplay between charge distribution and DNA in shaping HP1 paralog phase separation and localization DOI Creative Commons
Tien M. Phan,

Young C. Kim,

Galia T. Debelouchina

et al.

eLife, Journal Year: 2023, Volume and Issue: 12

Published: Oct. 5, 2023

The heterochromatin protein 1 (HP1) family is a crucial component of with diverse functions in gene regulation, cell cycle control, and differentiation. In humans, there are three paralogs, HP1α, HP1β, HP1γ, which exhibit remarkable similarities their domain architecture sequence properties. Nevertheless, these paralogs display distinct behaviors liquid-liquid phase separation (LLPS), process linked to formation. Here, we employ coarse-grained simulation framework uncover the features responsible for observed differences LLPS. We highlight significance net charge patterning along governing paralog LLPS propensities. also show that both highly conserved folded less-conserved disordered domains contribute differences. Furthermore, explore potential co-localization different HP1 multicomponent assemblies impact DNA on this process. Importantly, our study reveals can significantly reshape stability minimal condensate formed by due competitive interactions HP1α HP1β HP1γ versus DNA. conclusion, work highlights physicochemical nature govern phase-separation provides molecular understanding role chromatin organization.

Language: Английский

Expanding the molecular language of protein liquid–liquid phase separation DOI
Shiv Rekhi, Cristobal Garcia Garcia,

Mayur Barai

et al.

Nature Chemistry, Journal Year: 2024, Volume and Issue: 16(7), P. 1113 - 1124

Published: March 29, 2024

Language: Английский

Citations

85
Sequence-dependent material properties of biomolecular condensates and their relation to dilute phase conformations DOI Creative Commons
Dinesh Sundaravadivelu Devarajan, Jiahui Wang, Beata Szała-Mendyk

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: March 1, 2024

Abstract Material properties of phase-separated biomolecular condensates, enriched with disordered proteins, dictate many cellular functions. Contrary to the progress made in understanding sequence-dependent phase separation little is known about sequence determinants condensate material properties. Using hydropathy scale and Martini models, we computationally decipher these relationships for charge-rich protein condensates. Our computations yield dynamical, rheological, interfacial condensates that are quantitatively comparable experimentally characterized Interestingly, find model natural proteins respond similarly charge segregation, despite different compositions. Molecular interactions within closely resemble those single-chain ensembles. Consequently, strongly correlate molecular contact dynamics structural We demonstrate potential harness characteristics predicting engineering functional insights from dilute

Language: Английский

Citations

47
Heterotypic electrostatic interactions control complex phase separation of tau and prion into multiphasic condensates and co-aggregates DOI Creative Commons

K. Sandeep,

Roopali Khanna,

Anamika Avni

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(2)

Published: Jan. 3, 2023

Biomolecular condensates formed via phase separation of proteins and nucleic acids are thought to perform a wide range critical cellular functions by maintaining spatiotemporal regulation organizing intracellular biochemistry. However, aberrant transitions implicated in multitude human diseases. Here, we demonstrate that two neuronal proteins, namely tau prion, undergo complex coacervation driven domain-specific electrostatic interactions yield highly dynamic, mesoscopic liquid-like droplets. The acidic N-terminal segment interacts electrostatically with the polybasic intrinsically disordered prion protein (PrP). We employed unique combination time-resolved tools encompass several orders magnitude timescales ranging from nanoseconds seconds. These studies unveil an intriguing symphony molecular events associated formation heterotypic comprising ephemeral, domain-specific, short-range nanoclusters. Our results reveal these can be tuned RNA stoichiometry-dependent manner resulting reversible, multiphasic, immiscible, ternary different morphologies core-shell nested This system exhibits typical three-regime behavior reminiscent other membraneless organelles including nucleolar condensates. also show upon aging, tau:PrP droplets gradually convert into solid-like co-assemblies sequestration persistent intermolecular interactions. vibrational Raman conjunction atomic force microscopy multi-color fluorescence imaging presence amorphous amyloid-like co-aggregates maturation. findings provide mechanistic underpinnings overlapping neuropathology involving PrP highlight broader biological role physiology disease.

Language: Английский

Citations

45
Determinants that enable disordered protein assembly into discrete condensed phases DOI
Rachel M. Welles, Kandarp A. Sojitra, Mikael V. Garabedian

et al.

Nature Chemistry, Journal Year: 2024, Volume and Issue: 16(7), P. 1062 - 1072

Published: Feb. 5, 2024

Language: Английский

Citations

41
Analytical Formulation and Field-Theoretic Simulation of Sequence-Specific Phase Separation of Protein-Like Heteropolymers with Short- and Long-Spatial-Range Interactions DOI
Jonas Wessén, Suman Das, Tanmoy Pal

et al.

The Journal of Physical Chemistry B, Journal Year: 2022, Volume and Issue: 126(45), P. 9222 - 9245

Published: Nov. 7, 2022

A theory for sequence-dependent liquid–liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs) in the study biomolecular condensates is formulated by extending random approximation (RPA) and field-theoretic simulation (FTS) heteropolymers with spatially long-range Coulomb interactions to include fundamental effects short-range, hydrophobic-like between amino acid residues. To this end, short-range are modeled Yukawa multiple nonelectrostatic charges derived from an eigenvalue decomposition pairwise residue–residue contact energies. Chain excluded volume afforded incompressibility constraints. mean-field leads effective Flory−Huggins χ parameter, which, conjunction RPA, accounts contact-interaction composition sequence-pattern electrostatics IDP LLPS, whereas FTS based on formulation provides full sequence dependence both short- interactions. This general approach illustrated here applications variants a natural context several different amino-acid interaction schemes as well set model hydrophobic-polar sequences sharing same composition. Effectiveness methodology verified coarse-grained explicit-chain molecular dynamics simulations.

Language: Английский

Citations

47
A synergy between site-specific and transient interactions drives the phase separation of a disordered, low-complexity domain DOI Creative Commons
Priyesh Mohanty,

Jayakrishna Shenoy,

Azamat Rizuan

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(34)

Published: Aug. 14, 2023

TAR DNA-binding protein 43 (TDP-43) is involved in key processes RNA metabolism and frequently implicated many neurodegenerative diseases, including amyotrophic lateral sclerosis frontotemporal dementia. The prion-like, disordered C-terminal domain (CTD) of TDP-43 aggregation-prone, can undergo liquid-liquid phase separation (LLPS) isolation, critical for (PS) the full-length under physiological conditions. While a short conserved helical region (CR, spanning residues 319-341) promotes oligomerization essential LLPS, aromatic flanking regions (QN-rich, IDR1/2) are also found to play role PS aggregation. Compared with other phase-separating proteins, CTD has notably distinct sequence composition aliphatic such as methionine leucine. Aliphatic were previously suggested modulate apparent viscosity resulting phases, but their direct contribution toward been relatively ignored. Using multiscale simulations coupled vitro saturation concentration (csat) measurements, we identified importance while suggesting an promoting single-chain compaction LLPS. Surprisingly, NMR experiments showed that transient interactions involving phenylalanine directly enhance site-specific, CR-mediated intermolecular association. Overall, our work highlights underappreciated mode biomolecular recognition, wherein both site-specific hydrophobic act synergistically drive disordered, low-complexity domain.

Language: Английский

Citations

38
Expanding the molecular language of protein liquid-liquid phase separation DOI Creative Commons
Shiv Rekhi, Cristobal Garcia Garcia,

Mayur Barai

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: March 3, 2023

Abstract Understanding the relationship between an amino acid sequence and its phase separation has important implications for analyzing cellular function, treating disease, designing novel biomaterials. Several features have been identified as drivers protein liquid-liquid (LLPS), leading to development of a “molecular grammar” LLPS. In this work, we further probed how modulates material properties resulting condensates. Specifically, used model intrinsically disordered polypeptide composed 8-residue repeat unit performed systematic manipulations targeting previously overlooked in literature. We generated sequences with no charged residues, high net charge, glycine or devoid aromatic arginine residues. report that all but one twelve variants designed undergo LLPS, albeit different extents, despite significant differences composition. These results support hypothesis multiple interactions diverse residue pairs work tandem drive separation. Molecular simulations paint picture underlying molecular details involving various atomic mediated by not just handful types, most characterized changes inter-residue contacts variants, thereby developing more complete understanding contributions such hydrophobicity, aromaticity Further, find condensates formed behave like viscous fluids, large their viscosities. The presented study significantly advance current sequence-phase behavior sequence-material relationships help interpret, model, design assembly.

Language: Английский

Citations

33
Role of Strong Localized vs Weak Distributed Interactions in Disordered Protein Phase Separation DOI Creative Commons
Shiv Rekhi, Dinesh Sundaravadivelu Devarajan, Michael P. Howard

et al.

The Journal of Physical Chemistry B, Journal Year: 2023, Volume and Issue: 127(17), P. 3829 - 3838

Published: April 20, 2023

Interaction strength and localization are critical parameters controlling the single-chain condensed-state properties of intrinsically disordered proteins (IDPs). Here, we decipher these relationships using coarse-grained heteropolymers comprised hydrophobic (H) polar (P) monomers as model IDPs. We systematically vary fraction P XP employ two distinct particle-based models that include either strong localized attractions between only H–H pairs (HP model) or weak distributed both H–P (HP+ model). To compare different sequences models, first carefully tune attraction for all to match radius gyration. Interestingly, find this procedure produces similar conformational ensembles, nonbonded potential energies, chain-level dynamics single chains almost in with some deviations HP at large XP. However, observe a surprisingly rich phase behavior deviates from expectation similarity level will translate phase-separation propensity. Coexistence dilute dense phases is observed up model-dependent XP, despite presence favorable interchain interactions, which quantify second virial coefficient. Instead, limited number attractive sites (H monomers) leads self-assembly finite-sized clusters sizes depending on Our findings strongly suggest interactions favor formation liquid-like condensates over much larger range sequence compositions compared interactions.

Language: Английский

Citations

31
Multiscale simulations reveal TDP-43 molecular-level interactions driving condensation DOI Creative Commons
Helgi I. Ingólfsson, Azamat Rizuan, Xikun Liu

et al.

Biophysical Journal, Journal Year: 2023, Volume and Issue: 122(22), P. 4370 - 4381

Published: Oct. 17, 2023

The RNA-binding protein TDP-43 is associated with mRNA processing and transport from the nucleus to cytoplasm. localizes in as well accumulating cytoplasmic condensates such stress granules. Aggregation formation of amyloid-like fibrils are hallmarks numerous neurodegenerative diseases, most strikingly present >90% amyotrophic lateral sclerosis (ALS) patients. If excessive accumulation causes, or caused by, neurodegeneration presently not known. In this work, we use molecular dynamics simulations at multiple resolutions explore self- cross-interaction dynamics. A full-length model TDP-43, all 414 amino acids, was constructed select structures functional domains (N-terminal domain, two RNA recognition motifs, RRM1 RRM2) modeling disordered connecting loops low complexity glycine-rich C-terminus domain. All-atom CHARMM36m single proteins served guides construct a coarse-grained Martini 3 TDP-43. coarser implicit solvent C⍺ model, optimized for proteins, were subsequently used probe interactions; self-interactions single-chain simulations, cross-interactions assemblies dozens hundreds proteins. Our findings illustrate utility different scales accessing molecular-level interactions suggest that has interaction preferences patterns, exhibiting an overall strong, but dynamic, association driving biomolecular condensates.

Language: Английский

Citations

25
Conformational Properties of Polymers at Droplet Interfaces as Model Systems for Disordered Proteins DOI Creative Commons
Jiahui Wang, Dinesh Sundaravadivelu Devarajan, Arash Nikoubashman

et al.

ACS Macro Letters, Journal Year: 2023, Volume and Issue: 12(11), P. 1472 - 1478

Published: Oct. 19, 2023

Polymer models serve as useful tools for studying the formation and physical properties of biomolecular condensates. In recent years, interface dividing dense dilute phases condensates has been discovered to be closely related their functionality, but conformational preferences constituent proteins remain unclear. To elucidate this, we perform molecular simulations a droplet formed by phase separation homopolymers surrogate model prion-like low-complexity domains. By systematically analyzing polymer conformations at different locations in droplet, find that chains become compact compared with interior. Further, segmental analysis revealed end sections are enriched maximize entropy more expanded than middle chains. We majority chain segments lie tangential surface, only ends tend align perpendicular interface. These trends also hold natural FUS LC LAF-1 RGG, which exhibit Our findings provide important insights into interfacial highlight value using simple physics understand underlying mechanisms.

Language: Английский

Citations

24