DOI: 10.1073/pnas.0511130103. Core domain interactions in full-length p53 in solution

Core domain interactions in full-length p53 in solution

10.1073/pnas.0511130103

Crossref journal-article

Proceedings of the National Academy of Sciences

Proceedings of the National Academy of Sciences (341)

Abstract

The tumor suppressor p53 consists of four 393-residue chains, each of which has two natively unfolded (N- and C-terminal) and two folded (core and tetramerization) domains. Their structural organization is poorly characterized as the protein tends to aggregate, has defied crystallization, and is at the limits of NMR studies. We first stabilized the protein by mutation to make it more suitable for extended study and then acquired NMR spectra on full-length protein and various combinations of shorter domain constructs. The NMR spectrum ( 15 N, 1 H transverse relaxation optimized spectroscopy) of full-length p53 was close to that expected from the sum of the spectra of isolated individual domains. However, patterns of changes in chemical shifts revealed unexpected interactions between the core domains. We used the NMR data as constraints in docking algorithms and found a previously uncharacterized self-complementary surface for the association of core domains into dimers within the tetrameric complex. Binding to DNA requires about a 70° rotation to break those subunit interactions and form the known protein:protein interface in the p53–DNA complex. We verified the interactions by the effects of mutation on DNA binding. Spectroscopic, biophysical, and mutational data conspired to give a picture of the p53 tetramer as a dimer of loosely tethered core dimers of appropriate symmetry to be poised to bind target DNA.

Bibliography

Veprintsev, D. B., Freund, S. M. V., Andreeva, A., Rutledge, S. E., Tidow, H., CaÃ±adillas, J. M. P., Blair, C. M., & Fersht, A. R. (2006). Core domain interactions in full-length p53 in solution. Proceedings of the National Academy of Sciences, 103(7), 2115â2119.

Authors 8

Dmitry B. Veprintsev (first)
Stefan M. V. Freund (additional)
Antonina Andreeva (additional)
Stacey E. Rutledge (additional)
Henning Tidow (additional)
José Manuel Pérez Cañadillas (additional)
Caroline M. Blair (additional)
Alan R. Fersht (additional)

References 34 Referenced 86

Dates

Type	When
Created	19 years, 6 months ago (Feb. 6, 2006, 8:33 p.m.)
Deposited	3 years, 4 months ago (April 12, 2022, 2:08 p.m.)
Indexed	2 months, 2 weeks ago (June 6, 2025, 8:46 a.m.)
Issued	19 years, 6 months ago (Feb. 6, 2006)
Published	19 years, 6 months ago (Feb. 6, 2006)
Published Online	19 years, 6 months ago (Feb. 6, 2006)
Published Print	19 years, 6 months ago (Feb. 14, 2006)

Funders 0

None

BibTeX

@article{Veprintsev_2006, title={Core domain interactions in full-length p53 in solution}, volume={103}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.0511130103}, DOI={10.1073/pnas.0511130103}, number={7}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Veprintsev, Dmitry B. and Freund, Stefan M. V. and Andreeva, Antonina and Rutledge, Stacey E. and Tidow, Henning and Cañadillas, José Manuel Pérez and Blair, Caroline M. and Fersht, Alan R.}, year={2006}, month=feb, pages={2115–2119} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        6,
        6
      ]
    ],
    "date-time": "2025-06-06T12:46:10Z",
    "timestamp": 1749213970797
  },
  "reference-count": 34,
  "publisher": "Proceedings of the National Academy of Sciences",
  "issue": "7",
  "content-domain": {
    "domain": [
      "www.pnas.org"
    ],
    "crossmark-restriction": true
  },
  "published-print": {
    "date-parts": [
      [
        2006,
        2,
        14
      ]
    ]
  },
  "abstract": "<jats:p>\n            The tumor suppressor p53 consists of four 393-residue chains, each of which has two natively unfolded (N- and C-terminal) and two folded (core and tetramerization) domains. Their structural organization is poorly characterized as the protein tends to aggregate, has defied crystallization, and is at the limits of NMR studies. We first stabilized the protein by mutation to make it more suitable for extended study and then acquired NMR spectra on full-length protein and various combinations of shorter domain constructs. The NMR spectrum (\n            <jats:sup>15</jats:sup>\n            N,\n            <jats:sup>1</jats:sup>\n            H transverse relaxation optimized spectroscopy) of full-length p53 was close to that expected from the sum of the spectra of isolated individual domains. However, patterns of changes in chemical shifts revealed unexpected interactions between the core domains. We used the NMR data as constraints in docking algorithms and found a previously uncharacterized self-complementary surface for the association of core domains into dimers within the tetrameric complex. Binding to DNA requires about a 70\u00b0 rotation to break those subunit interactions and form the known protein:protein interface in the p53\u2013DNA complex. We verified the interactions by the effects of mutation on DNA binding. Spectroscopic, biophysical, and mutational data conspired to give a picture of the p53 tetramer as a dimer of loosely tethered core dimers of appropriate symmetry to be poised to bind target DNA.\n          </jats:p>",
  "DOI": "10.1073/pnas.0511130103",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2006,
        2,
        7
      ]
    ],
    "date-time": "2006-02-07T01:33:05Z",
    "timestamp": 1139275985000
  },
  "page": "2115-2119",
  "update-policy": "http://dx.doi.org/10.1073/pnas.cm10313",
  "source": "Crossref",
  "is-referenced-by-count": 86,
  "title": "Core domain interactions in full-length p53 in solution",
  "prefix": "10.1073",
  "volume": "103",
  "author": [
    {
      "given": "Dmitry B.",
      "family": "Veprintsev",
      "sequence": "first",
      "affiliation": [
        {
          "name": "Medical Research Council Centre for Protein Engineering, Medical Research Council Centre, Hills Road, Cambridge CB2 2QH, United Kingdom"
        }
      ]
    },
    {
      "given": "Stefan M. V.",
      "family": "Freund",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Medical Research Council Centre for Protein Engineering, Medical Research Council Centre, Hills Road, Cambridge CB2 2QH, United Kingdom"
        }
      ]
    },
    {
      "given": "Antonina",
      "family": "Andreeva",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Medical Research Council Centre for Protein Engineering, Medical Research Council Centre, Hills Road, Cambridge CB2 2QH, United Kingdom"
        }
      ]
    },
    {
      "given": "Stacey E.",
      "family": "Rutledge",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Medical Research Council Centre for Protein Engineering, Medical Research Council Centre, Hills Road, Cambridge CB2 2QH, United Kingdom"
        }
      ]
    },
    {
      "given": "Henning",
      "family": "Tidow",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Medical Research Council Centre for Protein Engineering, Medical Research Council Centre, Hills Road, Cambridge CB2 2QH, United Kingdom"
        }
      ]
    },
    {
      "given": "Jos\u00e9 Manuel P\u00e9rez",
      "family": "Ca\u00f1adillas",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Medical Research Council Centre for Protein Engineering, Medical Research Council Centre, Hills Road, Cambridge CB2 2QH, United Kingdom"
        }
      ]
    },
    {
      "given": "Caroline M.",
      "family": "Blair",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Medical Research Council Centre for Protein Engineering, Medical Research Council Centre, Hills Road, Cambridge CB2 2QH, United Kingdom"
        }
      ]
    },
    {
      "given": "Alan R.",
      "family": "Fersht",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Medical Research Council Centre for Protein Engineering, Medical Research Council Centre, Hills Road, Cambridge CB2 2QH, United Kingdom"
        }
      ]
    }
  ],
  "member": "341",
  "published-online": {
    "date-parts": [
      [
        2006,
        2,
        6
      ]
    ]
  },
  "reference": [
    {
      "key": "e_1_3_3_1_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/35042675"
    },
    {
      "key": "e_1_3_3_2_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nrc864"
    },
    {
      "key": "e_1_3_3_3_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.2144363"
    },
    {
      "key": "e_1_3_3_4_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.95.11.6079"
    },
    {
      "key": "e_1_3_3_5_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.8023157"
    },
    {
      "key": "e_1_3_3_6_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nsb0495-321"
    },
    {
      "key": "e_1_3_3_7_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nsb0901-730"
    },
    {
      "key": "e_1_3_3_8_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/bi970759w"
    },
    {
      "key": "e_1_3_3_9_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1074/jbc.M500179200"
    },
    {
      "key": "e_1_3_3_10_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nsb1294-877"
    },
    {
      "key": "e_1_3_3_11_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1074/jbc.M003107200"
    },
    {
      "key": "e_1_3_3_12_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/j.jmb.2003.08.008"
    },
    {
      "key": "e_1_3_3_13_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.274.5289.948"
    },
    {
      "key": "e_1_3_3_14_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/bi035718g"
    },
    {
      "key": "e_1_3_3_15_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nsb0901-756"
    },
    {
      "key": "e_1_3_3_16_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/j.jmb.2004.07.042"
    },
    {
      "key": "e_1_3_3_17_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1023/A:1008317825976"
    },
    {
      "key": "e_1_3_3_18_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.95.25.14675"
    },
    {
      "key": "e_1_3_3_19_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1074/jbc.M309732200"
    },
    {
      "key": "e_1_3_3_20_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0022-2836(02)00326-1"
    },
    {
      "key": "e_1_3_3_21_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1074/jbc.M107516200"
    },
    {
      "key": "e_1_3_3_22_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.94.23.12366"
    },
    {
      "key": "e_1_3_3_23_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.96.15.8438"
    },
    {
      "key": "e_1_3_3_24_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/ng0492-45"
    },
    {
      "key": "e_1_3_3_25_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1128/mcb.12.6.2866-2871.1992"
    },
    {
      "key": "e_1_3_3_26_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1074/jbc.272.23.14830"
    },
    {
      "key": "e_1_3_3_27_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/protein/14.4.233"
    },
    {
      "key": "e_1_3_3_28_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/anie.200501887"
    },
    {
      "key": "e_1_3_3_29_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/j.jmb.2004.06.071"
    },
    {
      "key": "e_1_3_3_30_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/jm9703404"
    },
    {
      "key": "e_1_3_3_31_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/jmbi.1997.1203"
    },
    {
      "key": "e_1_3_3_32_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/jmbi.1996.0399"
    },
    {
      "key": "e_1_3_3_33_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/(SICI)1097-0134(19990515)35:3<364::AID-PROT11>3.0.CO;2-4"
    },
    {
      "key": "e_1_3_3_34_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1110/ps.03154503"
    }
  ],
  "container-title": "Proceedings of the National Academy of Sciences",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://pnas.org/doi/pdf/10.1073/pnas.0511130103",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2022,
        4,
        12
      ]
    ],
    "date-time": "2022-04-12T18:08:53Z",
    "timestamp": 1649786933000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://pnas.org/doi/full/10.1073/pnas.0511130103"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2006,
        2,
        6
      ]
    ]
  },
  "references-count": 34,
  "journal-issue": {
    "issue": "7",
    "published-print": {
      "date-parts": [
        [
          2006,
          2,
          14
        ]
      ]
    }
  },
  "alternative-id": [
    "10.1073/pnas.0511130103"
  ],
  "URL": "http://dx.doi.org/10.1073/pnas.0511130103",
  "relation": {
    "has-review": [
      {
        "id-type": "doi",
        "id": "10.3410/f.1033153.375726",
        "asserted-by": "object"
      }
    ]
  },
  "ISSN": [
    "0027-8424",
    "1091-6490"
  ],
  "subject": [],
  "container-title-short": "Proc. Natl. Acad. Sci. U.S.A.",
  "published": {
    "date-parts": [
      [
        2006,
        2,
        6
      ]
    ]
  },
  "assertion": [
    {
      "value": "2006-02-06",
      "order": 2,
      "name": "published",
      "label": "Published",
      "group": {
        "name": "publication_history",
        "label": "Publication History"
      }
    }
  ]
}