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PreprintCited by 39Protein Structure and DynamicsAdvanced Physical and Chemical Molecular InteractionsRNA and protein synthesis mechanisms

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GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems

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Jung, Jaewoon, Tan, Cheng, Sugita, Yuji·2023·Nature Communications
DOI 10.1101/2023.08.24.554724PMC PMC11032353

Preprint — published as 10.1038/s41467-024-47654-1

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Abstract

Residue-level coarse-grained (CG) molecular dynamics (MD) simulation is widely used to investigate slow biological processes that involve multiple proteins, nucleic acids, and their complexes. Biomolecules in a large simulation system are distributed non-uniformly, limiting computational efficiency with conventional methods. Here, we develop a hierarchical domain decomposition scheme with dynamic load balancing for heterogeneous biomolecular systems to keep computational efficiency even after drastic changes in particle distribution. The new schemes are applied to intrinsically disordered protein (IDP) droplet fusions. The droplet shape changes correlate with mixing IDP chains from two droplets. We also simulate formations of large IDP droplets, whose sizes are almost equivalent to those observed in microscopy. The methods have been implemented in CGDYN of the GENESIS software, which provides a new tool for investigating mesoscopic biological phenomena using the residue-level CG models.

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Research works printed but not linked: 65

  1. 10.1021/acs.chemrev.6b00163 · DOI
  2. 10.1063/1.4818908 · DOI
  3. 10.1021/acs.accounts.5b00338 · DOI
  4. 10.1006/jmbi.2000.3693 · DOI
  5. 10.1073/pnas.1402768111 · DOI
  6. 10.1021/jacs.6b03729 · DOI
  7. 10.1016/j.jmb.2009.11.056 · DOI
  8. 10.1073/pnas.2005500117 · DOI
  9. 10.1093/nar/gky158 · DOI
  10. 2019, 1CPN: A coarse-grained multi-scale model of chromatin, J Chem Phys, 150, 215102, 10.1063/1.5092976 · DOI
  11. 10.1073/pnas.0604817103 · DOI
  12. 2021, Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy, Nat Comput Sci, 1, 732, 10.1038/s43588-021-00155-3 · DOI
  13. 10.1371/journal.pcbi.1005941 · DOI
  14. 10.7554/eLife.30294 · DOI · Paper page
  15. 10.1063/1.4897649 · DOI
  16. 10.1063/1.4822042 · DOI
  17. 10.1016/j.bpj.2008.09.061 · DOI
  18. 10.1021/jp071097f · DOI
  19. 10.1021/acs.jctc.8b00987 · DOI
  20. 10.1002/(SICI)1096-987X(199705)18:7<849::AID-JCC1>3.0.CO;2-R · DOI
  21. 10.1039/c4cs00048j · DOI
  22. 10.1002/prot.22645 · DOI
  23. 10.1002/jcc.20291 · DOI
  24. 10.1371/journal.pcbi.1005659 · DOI · Paper page
  25. 10.1002/jcc.20289 · DOI · Paper page
  26. 10.1016/j.commatsci.2019.109363 · DOI
  27. 10.1016/j.cpc.2021.108171 · DOI · Paper page
  28. 10.1021/ct2001045 · DOI
  29. 2015, GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations, Wiley Interdiscip Rev Comput Mol Sci, 5, 310, 10.1002/wcms.1220 · DOI
  30. 10.1002/JCC.24874 · DOI
  31. 2022, Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations, PLoS Comput Biol, 18, e1009578, 10.1371/journal.pcbi.1009578 · DOI
  32. 10.1126/science.aaw8653 · DOI · Paper page
  33. 2020, Sequence dependent phase separation of protein-polynucleotide mixtures elucidated using molecular simulations, Nucleic Acids Res, 48, 12593, 10.1093/nar/gkaa1099 · DOI
  34. 2022, Uncovering the statistical physics of 3D chromosomal organization using data-driven modeling, Curr Opin Struct Biol, 75, 102418, 10.1016/j.sbi.2022.102418 · DOI
  35. 2020, Computational approaches from polymer physics to investigate chromatin folding, Curr Opin Cell Biol, 64, 10, 10.1016/j.ceb.2020.01.002 · DOI
  36. 10.1002/jcc.23591 · DOI
  37. 10.1371/journal.pbio.3000632 · DOI
  38. 10.1073/pnas.1912055117 · DOI
  39. 2023, Highly Charged Proteins and Their Repulsive Interactions Antagonize Biomolecular Condensation, JACS Au, 3, 834, 10.1021/jacsau.2c00646 · DOI
  40. 10.1371/journal.pcbi.1008308 · DOI
  41. 10.1038/nrm.2017.7 · DOI
  42. 1996, in kdd, 96, 226
  43. 10.1073/pnas.1504822112 · DOI · Paper page
  44. 10.1126/science.1172046 · DOI
  45. 2019, Cytoplasmic TDP-43 De-mixing Independent of Stress Granules Drives Inhibition of Nuclear Import, Loss of Nuclear TDP-43, and Cell Death, Neuron, 102, 339, 10.1016/j.neuron.2019.02.038 · DOI
  46. 10.1073/pnas.1614462114 · DOI
  47. 10.1002/anie.202006711 · DOI
  48. 10.1126/science.aar7366 · DOI
  49. 10.1126/science.aar7432 · DOI
  50. 2021, Sequence-encoded and composition-dependent protein-RNA interactions control multiphasic condensate morphologies, Nat Commun, 12, 872, 10.1038/s41467-021-21089-4 · DOI
  51. 10.1073/pnas.1917569117 · DOI
  52. Sanchez-Burgos, I. , Espinosa, J.R. , Joseph, J.A. & Collepardo-Guevara, R. Valency and Binding Affinity Variations Can Regulate the Multilayered Organization of Protein Condensates with Many Components. Biomolecules 11 (2021). · DOI
  53. Deviri, D. & Safran, S.A. Physical theory of biological noise buffering by multicomponent phase separation. Proc Natl Acad Sci U S A 118 (2021). · DOI
  54. 2020, Multiphase Complex Coacervate Droplets, J Am Chem Soc, 142, 2905, 10.1021/jacs.9b11468 · DOI
  55. 2022, Multiphase organization is a second phase transition within multi-component biomolecular condensates, J Chem Phys, 156, 191104, 10.1063/5.0088004 · DOI
  56. 10.1016/j.tibs.2017.12.001 · DOI
  57. 2021, Paraspeckles are constructed as block copolymer micelles, EMBO J, 40, e107270, 10.15252/embj.2020107270 · DOI
  58. 10.1016/j.tcb.2021.03.001 · DOI
  59. 10.1126/science.aar4199 · DOI · Paper page
  60. 2018, Imaging dynamic and selective low-complexity domain interactions that control gene transcription, Science, 361, ear2555, 10.1126/science.aar2555 · DOI · Paper page
  61. 10.1126/science.aar3958 · DOI · Paper page
  62. 10.1016/S0009-2614(02)01735-9 · DOI
  63. 10.1109/TMTT.1971.1127617 · DOI
  64. 10.1021/ct300361j · DOI
  65. 10.1021/acs.jctc.8b00299 · DOI

Metadata

Authors
Jung, J., Tan, C., & Sugita, Y.
Affiliations
  • RIKEN (JP)
  • RIKEN Center for Computational Science (JP)
Corresponding author
Sugita, Yuji
ORCID
Venue
Nature Communications
Publisher
openRxiv
Published
2023-08-25
Volume
15
Issue
1
Pages
3370-3370
ISSN
2041-1723 (ISSN-L)
DOI
10.1101/2023.08.24.554724
PMC
PMC11032353
OpenAlex
W4394979883
Cited by
39
References
1
Citations by year
2026: 11 · 2025: 19 · 2024: 9
FWCI
5.31
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • Research Square (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Ministry of Education, Culture, Sports, Science and Technology (JPMXP1020200101, 21H05282, 19H05645, JPMXP1122714694, hp210177, JPMXP1020230327, 21H05249, hp200135)
  • Japan Society for the Promotion of Science (21H05249, JPMXP1020200101, JPMXP1020230327, 21H05282, JPMXP1122714694, 19H05645)
  • RIKEN (hp200028, hp210177, 19H05645, hp200135, hp230212)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords
dynamic load balancing, hierarchical domain decomposition, intrinsically disordered proteins, protein droplets, droplet fusion, Ostwald ripening
MeSH terms
Nucleic Acids, Proteins, Software, Molecular Dynamics Simulation

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