Molecular Dynamics Simulation on Regulation of Liquid-liquid Phase Separation of Repetitive Peptides

Overview

Journal Sci Rep

Specialty Science

Date 2024 Jun 11

PMID 38862770

Authors

Xiaojun Yang

Yanwei Wang

Guangcan Yang

Affiliations

Soon will be listed here.

Abstract

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.

References

Altmeyer M, Neelsen K, Teloni F, Pozdnyakova I, Pellegrino S, Grofte M . Liquid demixing of intrinsically disordered proteins is seeded by poly(ADP-ribose). Nat Commun. 2015; 6:8088. PMC: 4560800. DOI: 10.1038/ncomms9088. View

Benayad Z, von Bulow S, Stelzl L, Hummer G . Simulation of FUS Protein Condensates with an Adapted Coarse-Grained Model. J Chem Theory Comput. 2020; 17(1):525-537. PMC: 7872324. DOI: 10.1021/acs.jctc.0c01064. View

Wang Y, Xiang D, Chen S, Yang G . Comprehensive Regulation of Liquid-Liquid Phase Separation of Polypeptides. Molecules. 2023; 28(18). PMC: 10536796. DOI: 10.3390/molecules28186707. View

Dumetz A, Chockla A, Kaler E, Lenhoff A . Protein phase behavior in aqueous solutions: crystallization, liquid-liquid phase separation, gels, and aggregates. Biophys J. 2007; 94(2):570-83. PMC: 2157236. DOI: 10.1529/biophysj.107.116152. View

Das S, Amin A, Lin Y, Chan H . Coarse-grained residue-based models of disordered protein condensates: utility and limitations of simple charge pattern parameters. Phys Chem Chem Phys. 2018; 20(45):28558-28574. DOI: 10.1039/c8cp05095c. View

Alberti S, Gladfelter A, Mittag T . Considerations and Challenges in Studying Liquid-Liquid Phase Separation and Biomolecular Condensates. Cell. 2019; 176(3):419-434. PMC: 6445271. DOI: 10.1016/j.cell.2018.12.035. View

Mateju D, Franzmann T, Patel A, Kopach A, Boczek E, Maharana S . An aberrant phase transition of stress granules triggered by misfolded protein and prevented by chaperone function. EMBO J. 2017; 36(12):1669-1687. PMC: 5470046. DOI: 10.15252/embj.201695957. View

Dannenhoffer-Lafage T, Best R . A Data-Driven Hydrophobicity Scale for Predicting Liquid-Liquid Phase Separation of Proteins. J Phys Chem B. 2021; 125(16):4046-4056. DOI: 10.1021/acs.jpcb.0c11479. View

Mori K, Weng S, Arzberger T, May S, Rentzsch K, Kremmer E . The C9orf72 GGGGCC repeat is translated into aggregating dipeptide-repeat proteins in FTLD/ALS. Science. 2013; 339(6125):1335-8. DOI: 10.1126/science.1232927. View

10.

Hnisz D, Shrinivas K, Young R, Chakraborty A, Sharp P . A Phase Separation Model for Transcriptional Control. Cell. 2017; 169(1):13-23. PMC: 5432200. DOI: 10.1016/j.cell.2017.02.007. View

11.

Patel A, Lee H, Jawerth L, Maharana S, Jahnel M, Hein M . A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation. Cell. 2015; 162(5):1066-77. DOI: 10.1016/j.cell.2015.07.047. View

12.

Jiang X, Sun Y, Yang K, Yuan B, Velkov T, Wang L . Coarse-grained simulations uncover Gram-negative bacterial defense against polymyxins by the outer membrane. Comput Struct Biotechnol J. 2021; 19:3885-3891. PMC: 8441625. DOI: 10.1016/j.csbj.2021.06.051. View

13.

Renton A, Majounie E, Waite A, Simon-Sanchez J, Rollinson S, Gibbs J . A hexanucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-linked ALS-FTD. Neuron. 2011; 72(2):257-68. PMC: 3200438. DOI: 10.1016/j.neuron.2011.09.010. View

14.

Dignon G, Zheng W, Kim Y, Best R, Mittal J . Sequence determinants of protein phase behavior from a coarse-grained model. PLoS Comput Biol. 2018; 14(1):e1005941. PMC: 5798848. DOI: 10.1371/journal.pcbi.1005941. View

15.

Mori K, Arzberger T, Grasser F, Gijselinck I, May S, Rentzsch K . Bidirectional transcripts of the expanded C9orf72 hexanucleotide repeat are translated into aggregating dipeptide repeat proteins. Acta Neuropathol. 2013; 126(6):881-93. DOI: 10.1007/s00401-013-1189-3. View

16.

Regy R, Thompson J, Kim Y, Mittal J . Improved coarse-grained model for studying sequence dependent phase separation of disordered proteins. Protein Sci. 2021; 30(7):1371-1379. PMC: 8197430. DOI: 10.1002/pro.4094. View

17.

Krainer G, Welsh T, Joseph J, Espinosa J, Wittmann S, de Csillery E . Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions. Nat Commun. 2021; 12(1):1085. PMC: 7889641. DOI: 10.1038/s41467-021-21181-9. View

18.

Zu T, Gibbens B, Doty N, Gomes-Pereira M, Huguet A, Stone M . Non-ATG-initiated translation directed by microsatellite expansions. Proc Natl Acad Sci U S A. 2010; 108(1):260-5. PMC: 3017129. DOI: 10.1073/pnas.1013343108. View

19.

DeJesus-Hernandez M, Mackenzie I, Boeve B, Boxer A, Baker M, Rutherford N . Expanded GGGGCC hexanucleotide repeat in noncoding region of C9ORF72 causes chromosome 9p-linked FTD and ALS. Neuron. 2011; 72(2):245-56. PMC: 3202986. DOI: 10.1016/j.neuron.2011.09.011. View

20.

Kanekura K, Hayamizu Y, Kuroda M . Order controls disordered droplets: structure-function relationships in -derived poly(PR). Am J Physiol Cell Physiol. 2021; 322(2):C197-C204. DOI: 10.1152/ajpcell.00372.2021. View