DOI: 10.1073/pnas.222303299. φ value analysis of heterogeneity in pathways of allosteric transitions: Evidence for parallel pathways of ATP-induced conformational changes in a GroEL ring

φ value analysis of heterogeneity in pathways of allosteric transitions: Evidence for parallel pathways of ATP-induced conformational changes in a GroEL ring

10.1073/pnas.222303299

Crossref journal-article

Proceedings of the National Academy of Sciences

Proceedings of the National Academy of Sciences (341)

Abstract

What are the mechanisms of ligand-induced allosteric transitions in proteins? A powerful method to characterize pathways and transition states of reactions is φ value analysis. A φ value is the ratio between the changes on a perturbation (e.g., mutation) in the activation and equilibrium free energies of a reaction. Here, φ value analysis is used to characterize the ATP-induced allosteric transitions of GroEL by using changes in ATP concentration as perturbations. GroEL consists of two stacked back-to-back heptameric rings that bind ATP with positive cooperativity within rings and negative cooperativity between rings. Evidence is presented for the existence of parallel pathways for the allosteric transition of each ring. In both allosteric transitions, there is an abrupt ATP-dependent switch from a pathway with ATP-binding sites in the transition state that are very similar to those of the initial T state (φ = 0) to a pathway with a φ value of ≈0.3. The φ value procedure outlined here should be useful in mapping the energy landscape of allosteric transitions of other proteins.

Bibliography

Horovitz, A., Amir, A., Danziger, O., & Kafri, G. (2002). Ï value analysis of heterogeneity in pathways of allosteric transitions: Evidence for parallel pathways of ATP-induced conformational changes in a GroEL ring. Proceedings of the National Academy of Sciences, 99(22), 14095â14097.

Authors 4

Amnon Horovitz (first)
Amnon Amir (additional)
Oded Danziger (additional)
Galit Kafri (additional)

References 26 Referenced 21

Dates

Type	When
Created	22 years, 10 months ago (Oct. 29, 2002, 12:24 p.m.)
Deposited	3 years, 4 months ago (April 13, 2022, 7:55 a.m.)
Indexed	1 year, 5 months ago (March 4, 2024, 4:21 p.m.)
Issued	22 years, 10 months ago (Oct. 18, 2002)
Published	22 years, 10 months ago (Oct. 18, 2002)
Published Online	22 years, 10 months ago (Oct. 18, 2002)
Published Print	22 years, 10 months ago (Oct. 29, 2002)

Funders 0

None

BibTeX

@article{Horovitz_2002, title={φ value analysis of heterogeneity in pathways of allosteric transitions: Evidence for parallel pathways of ATP-induced conformational changes in a GroEL ring}, volume={99}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.222303299}, DOI={10.1073/pnas.222303299}, number={22}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Horovitz, Amnon and Amir, Amnon and Danziger, Oded and Kafri, Galit}, year={2002}, month=oct, pages={14095–14097} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2024,
        3,
        4
      ]
    ],
    "date-time": "2024-03-04T21:21:54Z",
    "timestamp": 1709587314184
  },
  "reference-count": 26,
  "publisher": "Proceedings of the National Academy of Sciences",
  "issue": "22",
  "content-domain": {
    "domain": [
      "www.pnas.org"
    ],
    "crossmark-restriction": true
  },
  "published-print": {
    "date-parts": [
      [
        2002,
        10,
        29
      ]
    ]
  },
  "abstract": "<jats:p>What are the mechanisms of ligand-induced allosteric transitions in proteins? A powerful method to characterize pathways and transition states of reactions is \u03c6 value analysis. A \u03c6 value is the ratio between the changes on a perturbation (e.g., mutation) in the activation and equilibrium free energies of a reaction. Here, \u03c6 value analysis is used to characterize the ATP-induced allosteric transitions of GroEL by using changes in ATP concentration as perturbations. GroEL consists of two stacked back-to-back heptameric rings that bind ATP with positive cooperativity within rings and negative cooperativity between rings. Evidence is presented for the existence of parallel pathways for the allosteric transition of each ring. In both allosteric transitions, there is an abrupt ATP-dependent switch from a pathway with ATP-binding sites in the transition state that are very similar to those of the initial T state (\u03c6 = 0) to a pathway with a \u03c6 value of \u22480.3. The \u03c6 value procedure outlined here should be useful in mapping the energy landscape of allosteric transitions of other proteins.</jats:p>",
  "DOI": "10.1073/pnas.222303299",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2002,
        10,
        29
      ]
    ],
    "date-time": "2002-10-29T17:24:11Z",
    "timestamp": 1035912251000
  },
  "page": "14095-14097",
  "update-policy": "http://dx.doi.org/10.1073/pnas.cm10313",
  "source": "Crossref",
  "is-referenced-by-count": 21,
  "title": "\u03c6 value analysis of heterogeneity in pathways of allosteric transitions: Evidence for parallel pathways of ATP-induced conformational changes in a GroEL ring",
  "prefix": "10.1073",
  "volume": "99",
  "author": [
    {
      "given": "Amnon",
      "family": "Horovitz",
      "sequence": "first",
      "affiliation": [
        {
          "name": "Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel"
        }
      ]
    },
    {
      "given": "Amnon",
      "family": "Amir",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel"
        }
      ]
    },
    {
      "given": "Oded",
      "family": "Danziger",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel"
        }
      ]
    },
    {
      "given": "Galit",
      "family": "Kafri",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel"
        }
      ]
    }
  ],
  "member": "341",
  "published-online": {
    "date-parts": [
      [
        2002,
        10,
        18
      ]
    ]
  },
  "reference": [
    {
      "key": "e_1_3_2_1_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1017/S0033583500003826"
    },
    {
      "key": "e_1_3_2_2_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1146/annurev.biochem.67.1.581"
    },
    {
      "key": "e_1_3_2_3_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1146/annurev.biophys.30.1.245"
    },
    {
      "key": "e_1_3_2_4_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/jsbi.2001.4377"
    },
    {
      "key": "e_1_3_2_5_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/371578a0"
    },
    {
      "key": "e_1_3_2_6_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0092-8674(00)81342-2"
    },
    {
      "key": "e_1_3_2_7_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0092-8674(01)00617-1"
    },
    {
      "key": "e_1_3_2_8_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/bi00016a001"
    },
    {
      "key": "e_1_3_2_9_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/jmbi.1996.0028"
    },
    {
      "key": "e_1_3_2_10_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/41944"
    },
    {
      "key": "e_1_3_2_11_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.117.3039.340"
    },
    {
      "key": "e_1_3_2_12_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0022-2836(92)90561-W"
    },
    {
      "key": "e_1_3_2_13_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/322284a0"
    },
    {
      "key": "e_1_3_2_14_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.88.10.4472"
    },
    {
      "key": "e_1_3_2_15_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1007/s004220050302"
    },
    {
      "key": "e_1_3_2_16_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/ja983136u"
    },
    {
      "key": "e_1_3_2_17_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/35001586"
    },
    {
      "key": "e_1_3_2_18_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/jmbi.2000.4014"
    },
    {
      "key": "e_1_3_2_19_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nsb0901-765"
    },
    {
      "key": "e_1_3_2_20_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.91.22.10426"
    },
    {
      "key": "e_1_3_2_21_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nsb723"
    },
    {
      "key": "e_1_3_2_22_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0022-2836(65)80285-6"
    },
    {
      "key": "e_1_3_2_23_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/j100879a039"
    },
    {
      "key": "e_1_3_2_24_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/bulm.1999.0150"
    },
    {
      "key": "e_1_3_2_25_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/bi980370o"
    },
    {
      "key": "e_1_3_2_26_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.94.5.1698"
    }
  ],
  "container-title": "Proceedings of the National Academy of Sciences",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://pnas.org/doi/pdf/10.1073/pnas.222303299",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2022,
        4,
        13
      ]
    ],
    "date-time": "2022-04-13T11:55:52Z",
    "timestamp": 1649850952000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://pnas.org/doi/full/10.1073/pnas.222303299"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2002,
        10,
        18
      ]
    ]
  },
  "references-count": 26,
  "journal-issue": {
    "issue": "22",
    "published-print": {
      "date-parts": [
        [
          2002,
          10,
          29
        ]
      ]
    }
  },
  "alternative-id": [
    "10.1073/pnas.222303299"
  ],
  "URL": "http://dx.doi.org/10.1073/pnas.222303299",
  "relation": {},
  "ISSN": [
    "0027-8424",
    "1091-6490"
  ],
  "subject": [],
  "container-title-short": "Proc. Natl. Acad. Sci. U.S.A.",
  "published": {
    "date-parts": [
      [
        2002,
        10,
        18
      ]
    ]
  },
  "assertion": [
    {
      "value": "2002-05-21",
      "order": 0,
      "name": "received",
      "label": "Received",
      "group": {
        "name": "publication_history",
        "label": "Publication History"
      }
    },
    {
      "value": "2002-10-18",
      "order": 2,
      "name": "published",
      "label": "Published",
      "group": {
        "name": "publication_history",
        "label": "Publication History"
      }
    }
  ]
}