Molecular dynamics simulation on regulation of liquid–liquid phase separation of repetitive peptides

Understanding the intricate interactions governing protein and peptide behavior in liquid–liquid phase separation (LLPS) is crucial for unraveling biological functions and dysfunctions. This study employs a residue-leveled coarse-grained molecular dynamics approach to simulate the phase separation o...

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Bibliographic Details
Published in:Scientific reports Vol. 14; no. 1; pp. 13382 - 10
Main Authors: Yang, Xiaojun, Wang, Yanwei, Yang, Guangcan
Format: Journal Article
Language:English
Published: London Nature Publishing Group UK 11.06.2024
Nature Publishing Group
Nature Portfolio
Subjects:
631/57/2266
631/57/2269
631/57/2272
Dielectric constant
DNA - chemistry
DNA - metabolism
Electrostatic interaction
Electrostatic properties
GENESIS
Humanities and Social Sciences
Hydrophobic and Hydrophilic Interactions
Hydrophobicity
Liquid–liquid phase separation
Molecular dynamics
Molecular Dynamics Simulation
multidisciplinary
Peptides
Peptides - chemistry
Phase Separation
Phase Transition
Polypeptides
Polyproline
Salts
Science
Science (multidisciplinary)
Temperature
Temperature effects
Liquid–liquid phase separation
Molecular dynamics
Polypeptides
Hydrophobicity
GENESIS
Electrostatic interaction
ISSN:2045-2322, 2045-2322
Online Access:Get full text
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Summary:Understanding the intricate interactions governing protein and peptide behavior in liquid–liquid phase separation (LLPS) is crucial for unraveling biological functions and dysfunctions. This study employs a residue-leveled coarse-grained molecular dynamics approach to simulate the phase separation of repetitive polyproline and polyarginine peptides (poly PR) with varying lengths and sequences in solution, considering different concentrations and temperatures. Our findings highlight the crucial role of sequence order in promoting LLPS in peptides with identical lengths of repetitive sequences. Interestingly, repetitive peptides containing fewer than 10 polyarginine repeats exhibit no LLPS, even at salt concentrations up to 3 M. Notably, our simulations align with experimental observations, pinpointing a salt concentration of 2.7 M for PR25-induced LLPS. Utilizing the same methodology, we predict the required salt concentrations for LLPS induction as 1.2 M, 1.5 M, and 2.7 M for PR12, PR15, and PR35, respectively. These predictions demonstrate good agreement with experimental results. Extending our investigation to include the peptide glutamine and arginine (GR15) in DNA solution, our simulations mirror experimental observations of phase separation. To unveil the molecular forces steering peptide phase separation, we introduce a dielectric constant modifier and hydrophobicity disruptor into poly PR systems. Our coarse-grained analysis includes an examination of temperature effects, leading to the inference that both hydrophobic and electrostatic interactions drive phase separation in peptide systems.
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ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-024-64327-7