Torsional stress can regulate the unwrapping of two outer half superhelical turns of nucleosomal DNA

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{
  "metadata": {
    "is_last": true, 
    "version": 1, 
    "title": "Torsional stress can regulate the unwrapping of two outer half superhelical turns of nucleosomal DNA", 
    "keywords": [
      "nucleosome", 
      "unwrapping", 
      "DNA", 
      "bendability", 
      "torsional stress"
    ], 
    "description": "Torsional stress has a significant impact on the structure and stability of the nucleosome.  RNA polymerase imposes torsional stress on the DNA in chromatin and unwraps the DNA from the nucleosome to access the genetic information encoded in the DNA.  To understand how the torsional stress affects the stability of the nucleosome, we examined the unwrapping of two half superhelical turns of nucleosomal DNA from either end of the DNA under torsional stress with all-atom molecular dynamics simulations.  The free energies for unwrapping the DNA indicate that positive stress that overtwists DNA facilitates a large-scale asymmetric unwrapping of the DNA without a large extension of the DNA.  During the unwrapping, one end of the DNA was dissociated from H3 and H2A-H2B while the other end of the DNA stably remained wrapped.  The detailed analysis indicates that this asymmetric dissociation is facilitated by the geometry and bendability of the DNA under positive stress.  The geometry stabilized the interaction between the major groove of the twisted DNA and the H3 \u03b1N-helix, and the straightened DNA destabilized the interaction with H2A-H2B.  Under negative stress, the DNA became more bendable and flexible, which facilitated the binding of the unwrapped DNA to the octamer in a stable state.  Consequently, we conclude that the torsional stress has a significant impact on the affinity of the DNA and the octamer through the inherent nature of the DNA, and can change the accessibility of regulatory proteins.", 
    "license": "Creative Commons Attribution 4.0 International", 
    "references": [
      {
        "url": "https://www.pnas.org/content/118/7/e2020452118", 
        "type": "Journal reference", 
        "citation": "H. Ishida, H. Kono, Proc. Natl. Acad. Sci. U.S.A. 118, e2020452118 (2021)", 
        "doi": "10.1073/pnas.2020452118"
      }
    ], 
    "doi": "10.24435/materialscloud:r9-xt", 
    "conceptrecid": "545", 
    "publication_date": "Jan 27, 2021, 09:49:18", 
    "edited_by": 216, 
    "_oai": {
      "id": "oai:materialscloud.org:546"
    }, 
    "contributors": [
      {
        "affiliations": [
          "National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan"
        ], 
        "email": "ishida.hisashi@qst.go.jp", 
        "familyname": "Ishida", 
        "givennames": "Hisashi"
      }, 
      {
        "affiliations": [
          "National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan"
        ], 
        "email": "kono.hidetoshi@qst.go.jp", 
        "familyname": "Kono", 
        "givennames": "Hidetoshi"
      }
    ], 
    "owner": 216, 
    "license_addendum": null, 
    "mcid": "2021.23", 
    "_files": [
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        "size": 3604, 
        "checksum": "md5:a82d6093544286fb7a58be1952a39a85", 
        "description": "README", 
        "key": "README.txt"
      }, 
      {
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        "checksum": "md5:3f7ef8c39c52add2082cb9946ac95968", 
        "description": "parameter/topology file (amber-format) to visualize the nucleosome using VMD software", 
        "key": "prmtop"
      }, 
      {
        "size": 322155, 
        "checksum": "md5:767758115ff19a176efd6d3f8a735478", 
        "description": "coordinate of the nucleosome (pdb-format) for Figure 1", 
        "key": "Figure1.tar.gz"
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        "checksum": "md5:eb94d768c893b9e0133fccdd001f8b9b", 
        "description": "coordinate of the nucleosoem (pdb-format) for Figure 3", 
        "key": "Figure3.tar.gz"
      }, 
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        "description": "trajectory of the nucleosome (mdcrd-format) under positive stress", 
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        "description": "trajectory of the nucleosome (mdcrd-format) under negative stress", 
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        "description": "trajectory of the nucleosome (mdcrd-format) under no stress", 
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    ], 
    "id": "546", 
    "status": "published"
  }, 
  "revision": 19, 
  "updated": "2021-02-09T01:46:17.395414+00:00", 
  "created": "2020-10-06T06:32:04.013770+00:00", 
  "id": "546"
}