4.5 Article

Phase separation in amino acid mixtures is governed by composition

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Chemistry, Multidisciplinary

Deciphering how naturally occurring sequence features impact the phase behaviours of disordered prion-like domains

Anne Bremer et al.

Summary: This study uncovers how evolutionarily conserved compositional biases influence the phase behavior of Prion-like low-complexity domains (PLCDs). Tyrosine is identified as a stronger sticker, while lysine weakens sticker-sticker interactions. Additionally, glycine and serine residues act as non-equivalent spacers, impacting the driving forces for phase separation in PLCDs.

NATURE CHEMISTRY (2022)

Article Multidisciplinary Sciences

Dilute phase oligomerization can oppose phase separation and modulate material properties of a ribonucleoprotein condensate

Ian Seim et al.

Summary: This study reveals a mechanism that influences the composition of ribonucleoprotein bodies, in which specific sequence motifs and synergies with the intrinsically disordered region drive the formation of oligomers in the dilute phase, hindering its incorporation into the dense phase. This finding provides new insights for designing synthetic ribonucleoprotein bodies.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

Article Biochemistry & Molecular Biology

A conceptual framework for understanding phase separation and addressing open questions and challenges

Tanja Mittag et al.

Summary: Macromolecular phase separation plays an important role in the spatial organization within cells. By understanding the synergy between networking and density transitions, we can explain the process of phase separation coupled to percolation (PSCP). This process forms viscoelastic network fluids with specific internal network structures, allowing for time-dependent interactions between viscous and elastic properties. PSCP provides insights into the role of macromolecular phase separation in biology by connecting different observations and addressing related challenges.

MOLECULAR CELL (2022)

Article Biochemistry & Molecular Biology

Clustering of Aromatic Residues in Prion-like Domains Can Tune the Formation, State, and Organization of Biomolecular Condensates

Alex S. Holehouse et al.

Summary: The research reveals that Velol protein forms solid-like assemblies in Balbiani bodies, and manipulating its structure or design can alter its internal dynamics, offering insights for the design of synthetic condensates.

BIOCHEMISTRY (2021)

Article Chemistry, Physical

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

Zakarya Benayad et al.

Summary: In this study, researchers developed a strategy to fine-tune the potential energy function for molecular dynamics simulations of biopolymer phase separation. By rebalancing protein-protein interactions against solvation and entropic contributions, they were able to simulate the liquid droplet formation of FUS low-complexity domain (LCD) with a rebalanced MARTINI model. The simulations successfully captured the phase separation of FUS-LCD droplets and provided insights into their physicochemical properties and dynamics.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

Article Biology

Charge-driven condensation of RNA and proteins suggests broad role of phase separation cytoplasmic environments

Bercem Dutagaci et al.

Summary: Phase separation processes, driven by electrostatic complementarity, have been shown to occur between RNA and positively charged proteins, suggesting a more general organizing principle for biological macromolecules in cellular environments. The resulting condensates retain internal dynamics and may occur widely in heterogeneous cellular environments between nucleic acid and protein components, without requiring polymer properties.
Article Chemistry, Physical

Salt dependent phase behavior of intrinsically disordered proteins from a coarse-grained model with explicit water and ions

Adiran Garaizar et al.

Summary: This work presents a novel approach to study the salt-dependent formation of biomolecular condensates by incorporating explicit water and salt in sequence-dependent coarse-grained models for proteins and RNA. The authors demonstrate that their model qualitatively captures experimental trends and behaviors, showing good agreement with reported in vitro phase behavior in different systems with varying salt concentrations. This work represents a significant step forward in extending sequence-dependent coarse-grained models to include water and salt in the study of biomolecular condensate self-assembly.

JOURNAL OF CHEMICAL PHYSICS (2021)

Article Multidisciplinary Sciences

Accurate model of liquid-liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties

Giulio Tesei et al.

Summary: Researchers have found that many intrinsically disordered proteins (IDPs) can participate in the formation of membraneless organelles in the cell. Investigating the phase behavior of IDPs through molecular simulations requires an accurate description of intramolecular and intermolecular interactions. By developing a coarse-grained model based on experimental data, the model accurately reproduces the conformational propensities of IDPs.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Article Biochemistry & Molecular Biology

Improved coarse-grained model for studying sequence dependent phase separation of disordered proteins

Roshan Mammen Regy et al.

Summary: The study presents improvements to the hydropathy scale model for simulating sequence-specific behavior of intrinsically disordered proteins, including liquid-liquid phase separation. By using the Urry hydropathy scale and introducing new model parameters, accurate simulations of protein LLPS can be achieved.

PROTEIN SCIENCE (2021)

Review Neurosciences

RNA modulates physiological and neuropathological protein phase transitions

Jacob R. Mann et al.

Summary: Aggregation of RNA-binding proteins is a pathological hallmark of neurodegenerative disorders like ALS and FTD. Recent studies suggest liquid-liquid phase separation may be a critical step in the formation of pathological inclusions. RNA, a common ligand of disease-linked RBPs, plays a crucial role in regulating RBP phase transitions, although it can also antagonize RBP phase behavior in certain conditions.

NEURON (2021)

Article Computer Science, Interdisciplinary Applications

Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy

Jerelle A. Joseph et al.

Summary: Mpipi is a multiscale coarse-grained protein model that quantitatively describes the change in protein critical temperatures with respect to amino acid sequence, considering the dominant role of pi-pi and hybrid cation-pi/pi-pi interactions, and the stronger attractive contacts of arginines compared to lysines. Experimental benchmarks demonstrate that Mpipi predictions are in good agreement with experimental results, and the model can accurately predict protein-RNA interactions and liquid-liquid phase separation trends of proteins with sequence mutations.

NATURE COMPUTATIONAL SCIENCE (2021)

Article Chemistry, Multidisciplinary

Prediction and characterization of liquid-liquid phase separation of minimalistic peptides

Yiming Tang et al.

Summary: This study comprehensively explores the abilities of all 400 dipeptide combinations to undergo LLPS and validates the predictions, demonstrating that dipeptides possess multivalent interactions sufficient for LLPS. This paves the way for predicting and characterizing peptide phase behavior at the molecular level.

CELL REPORTS PHYSICAL SCIENCE (2021)

Article Biophysics

Physical Principles Underlying the Complex Biology of Intracellular Phase Transitions

Jeong-Mo Choi et al.

Annual Review of Biophysics (2020)

Article Chemistry, Physical

Development of a Force Field for the Simulation of Single-Chain Proteins and Protein-Protein Complexes

Stefano Piana et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)

Article Chemistry, Physical

Biomolecular Phase Separation: From Molecular Driving Forces to Macroscopic Properties

Gregory L. Dignon et al.

Annual Review of Physical Chemistry (2020)

Article Multidisciplinary Sciences

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

Jorge R. Espinosa et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Review Multidisciplinary Sciences

Beyond aggregation: Pathological phase transitions in neurodegenerative disease

Cecile Mathieu et al.

SCIENCE (2020)

Article Chemistry, Physical

Molecular Details of Protein Condensates Probed by Microsecond Long Atomistic Simulations

Wenwei Zheng et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2020)

Article Chemistry, Multidisciplinary

Nucleation and Growth of Amino Acid and Peptide Supramolecular Polymers through Liquid-Liquid Phase Separation

Chengqian Yuan et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2019)

Article Biochemistry & Molecular Biology

Relationship of Sequence and Phase Separation in Protein Low Complexity Regions

Erik W. Martin et al.

BIOCHEMISTRY (2018)

Article Biochemistry & Molecular Biology

Theories for Sequence-Dependent Phase Behaviors of Biomolecular Condensates

Yi-Hsuan Lin et al.

BIOCHEMISTRY (2018)

Article Chemistry, Physical

Peptide Solubility Limits: Backbone and Side-Chain Interactions

Rahul Sarma et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2018)

Article Multidisciplinary Sciences

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

Paul Robustelli et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Biochemical Research Methods

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

Gregory L. Dignon et al.

PLOS COMPUTATIONAL BIOLOGY (2018)

Article Multidisciplinary Sciences

Relation between single-molecule properties and phase behavior of intrinsically disordered proteins

Gregory L. Dignon et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Biochemistry & Molecular Biology

Intrinsically disordered sequences enable modulation of protein phase separation through distributed tyrosine motifs

Yuan Lin et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2017)

Article Chemistry, Multidisciplinary

Liquid-Liquid Phase Separation in Oligomeric Peptide Solutions

Ying Wang et al.

LANGMUIR (2017)

Review Cell Biology

Biomolecular condensates: organizers of cellular biochemistry

Salman F. Banani et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2017)

Review Multidisciplinary Sciences

Liquid phase condensation in cell physiology and disease

Yongdae Shin et al.

SCIENCE (2017)

Article Biology

The liquid structure of elastin

Sarah Rauscher et al.

Article Biophysics

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

Robert T. McGibbon et al.

BIOPHYSICAL JOURNAL (2015)

Article Chemistry, Physical

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

Stefano Piana et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2015)

Article Physics, Multidisciplinary

Polymer physics of intracellular phase transitions

Clifford P. Brangwynne et al.

NATURE PHYSICS (2015)

Article Chemistry, Physical

Solubility and Aggregation of Gly5 in Water

Deepti Karandur et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2014)

Article Chemistry, Multidisciplinary

An overview of the Amber biomolecular simulation package

Romelia Salomon-Ferrer et al.

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2013)

Article Multidisciplinary Sciences

Phase transitions in the assembly of multivalent signalling proteins

Pilong Li et al.

NATURE (2012)

Article Chemistry, Physical

Virtual Screening for Dipeptide Aggregation: Toward Predictive Tools for Peptide Self-Assembly

Pim W. J. M. Frederix et al.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2011)

Article Biochemistry & Molecular Biology

Improved side-chain torsion potentials for the Amber ff99SB protein force field

Kresten Lindorff-Larsen et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)

Article Chemistry, Multidisciplinary

PACKMOL: A Package for Building Initial Configurations for Molecular Dynamics Simulations

L. Martinez et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)

Article Chemistry, Physical

Optimized Molecular Dynamics Force Fields Applied to the Helix-Coil Transition of Polypeptides

Robert B. Best et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2009)

Article Chemistry, Physical

The MARTINI force field: Coarse grained model for biomolecular simulations

Siewert J. Marrink et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2007)

Article Chemistry, Physical

Canonical sampling through velocity rescaling

Giovanni Bussi et al.

JOURNAL OF CHEMICAL PHYSICS (2007)