DOI: 10.1002/prot.340110406. Protein‐protein recognition analyzed by docking simulation

Protein‐protein recognition analyzed by docking simulation

10.1002/prot.340110406

Crossref journal-article

Wiley

Proteins: Structure, Function, and Bioinformatics (311)

Abstract

AbstractAntibody–lysozyme and protease–inhibitor complexes are reconstituted by docking lysozyme as a rigid body onto the combining site of the antibodies and the inhibitors onto the active site of the proteases. Simplified protein models with one sphere per residue are subjected to simulated annealing using a crude energy function where the attractive component is proportional to the interface area. The procedure finds clusters of orientations in which a steric fit between the two protein components is achieved over a large contact surface. With five out of six complexes, the native structure of the complexes determined by X‐ray crystallography is among those retained. Docked complexes are then subjected to conformational energy refinement with full atomic detail. With Fab HyHEL 5 and lysozyme, a native‐like complex has the lowest refined energy. It can also be retrieved when starting with the X‐ray structure of free lysozyme. However, some non‐native complexes cannot be rejected: they form large interfaces, have a large number of H‐bonds, and few unpaired polar groups. While these are necessary features of protein–protein recognition, they are not sufficient in determining specificity.

Bibliography

Cherfils, J., Duquerroy, S., & Janin, J. (1991). Proteinâprotein recognition analyzed by docking simulation. Proteins: Structure, Function, and Bioinformatics, 11(4), 271â280. Portico.

Authors 3

Jacqueline Cherfils (first)
Stéphane Duquerroy (additional)
Joël Janin (additional)

References 46 Referenced 113

10.1016/S0021-9258(17)46181-3 / J. Biol. Chem. / The structure of protein‐protein recognition sites by Janin J. (1990)
10.1038/256705a0
10.1016/S0021-9258(18)38002-5 / J. Biol. Chem. / Antibody‐antigen complexes by Davies D. R. (1988)
10.1146/annurev.bb.16.060187.001035
10.1016/0022-2836(78)90302-9
10.1002/bip.360240307
10.1016/0079-6107(87)90008-3
10.1016/0022-2836(76)90004-8
10.1073/pnas.72.4.1330
10.1073/pnas.84.22.8075
10.1073/pnas.86.15.5938
10.1126/science.2426778
10.1016/0022-2836(74)90163-6
10.1002/j.1460-2075.1986.tb04286.x / EMBO J / Refined 1.2 Å structure of the complex formed between subtilisin Carlsberg and the inhibitor eglin c. Molecular structure of eglin and its detailed interaction with subtilisin by Bode W. (1986)
10.1002/j.1460-2075.1986.tb04521.x
10.1016/S0022-2836(77)80200-3
10.1016/0022-2836(73)90011-9
10.1016/0022-2836(71)90324-X
10.1073/pnas.77.4.1736
10.1038/248338a0
10.1126/science.2011744
10.1063/1.1699114
10.1126/science.220.4598.671
10.1007/978-94-015-7744-1
{'key': 'e_1_2_1_26_2', 'volume-title': 'X‐PLOR Version 1.5 Manual', 'author': 'Brünger A.', 'year': '1987'} / X‐PLOR Version 1.5 Manual by Brünger A. (1987)
10.1002/jcc.540040211
10.1016/0022-2836(74)90598-1
10.1107/S010876818300275X
10.1016/0022-2836(72)90028-9
{'key': 'e_1_2_1_31_2', 'first-page': '417', 'article-title': 'Structure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor', 'volume': '77', 'author': 'Rühlmann A.', 'year': '1973', 'journal-title': 'Crystal structure determination and stereochemistry of the contact region. J. Mol. Biol.'} / Crystal structure determination and stereochemistry of the contact region. J. Mol. Biol. / Structure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor by Rühlmann A. (1973)
10.1016/0022-2836(76)90334-X
10.1016/0022-2836(89)90487-7
10.1073/pnas.75.1.303
10.1016/0022-2836(82)90153-X
10.1002/bip.360240814
10.1002/bip.360250705
10.1016/0022-2836(91)90859-5
10.1021/jm00399a006
10.1038/319199a0
10.1021/bi00375a028
10.4049/jimmunol.128.1.314 / J. Immunol. / Mapping the antigenic epitope for a monoclonal antibody against lysozyme by Smith‐Gill S. J. (1982)
10.1016/0161-5890(87)90081-2
10.1038/314235a0
10.1126/science.3810155
10.1021/bi00437a034
10.1038/348254a0

Dates

Type	When
Created	20 years, 3 months ago (May 28, 2005, 9:13 p.m.)
Deposited	1 year, 10 months ago (Oct. 23, 2023, 3:43 a.m.)
Indexed	1 month, 4 weeks ago (July 1, 2025, 9:07 a.m.)
Issued	33 years, 8 months ago (Dec. 1, 1991)
Published	33 years, 8 months ago (Dec. 1, 1991)
Published Online	21 years, 6 months ago (Feb. 3, 2004)
Published Print	33 years, 8 months ago (Dec. 1, 1991)

Funders 0

None

BibTeX

@article{Cherfils_1991, title={Protein‐protein recognition analyzed by docking simulation}, volume={11}, ISSN={1097-0134}, url={http://dx.doi.org/10.1002/prot.340110406}, DOI={10.1002/prot.340110406}, number={4}, journal={Proteins: Structure, Function, and Bioinformatics}, publisher={Wiley}, author={Cherfils, Jacqueline and Duquerroy, Stéphane and Janin, Joël}, year={1991}, month=dec, pages={271–280} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        7,
        1
      ]
    ],
    "date-time": "2025-07-01T13:07:07Z",
    "timestamp": 1751375227975
  },
  "reference-count": 46,
  "publisher": "Wiley",
  "issue": "4",
  "license": [
    {
      "start": {
        "date-parts": [
          [
            2004,
            2,
            3
          ]
        ],
        "date-time": "2004-02-03T00:00:00Z",
        "timestamp": 1075766400000
      },
      "content-version": "vor",
      "delay-in-days": 4447,
      "URL": "http://onlinelibrary.wiley.com/termsAndConditions#vor"
    }
  ],
  "content-domain": {
    "domain": [],
    "crossmark-restriction": false
  },
  "published-print": {
    "date-parts": [
      [
        1991,
        12
      ]
    ]
  },
  "abstract": "<jats:title>Abstract</jats:title><jats:p>Antibody\u2013lysozyme and protease\u2013inhibitor complexes are reconstituted by docking lysozyme as a rigid body onto the combining site of the antibodies and the inhibitors onto the active site of the proteases. Simplified protein models with one sphere per residue are subjected to simulated annealing using a crude energy function where the attractive component is proportional to the interface area. The procedure finds clusters of orientations in which a steric fit between the two protein components is achieved over a large contact surface. With five out of six complexes, the native structure of the complexes determined by X\u2010ray crystallography is among those retained. Docked complexes are then subjected to conformational energy refinement with full atomic detail. With Fab HyHEL 5 and lysozyme, a native\u2010like complex has the lowest refined energy. It can also be retrieved when starting with the X\u2010ray structure of free lysozyme. However, some non\u2010native complexes cannot be rejected: they form large interfaces, have a large number of H\u2010bonds, and few unpaired polar groups. While these are necessary features of protein\u2013protein recognition, they are not sufficient in determining specificity.</jats:p>",
  "DOI": "10.1002/prot.340110406",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2005,
        5,
        29
      ]
    ],
    "date-time": "2005-05-29T01:13:37Z",
    "timestamp": 1117329217000
  },
  "page": "271-280",
  "source": "Crossref",
  "is-referenced-by-count": 113,
  "title": "Protein\u2010protein recognition analyzed by docking simulation",
  "prefix": "10.1002",
  "volume": "11",
  "author": [
    {
      "given": "Jacqueline",
      "family": "Cherfils",
      "sequence": "first",
      "affiliation": []
    },
    {
      "given": "St\u00e9phane",
      "family": "Duquerroy",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Jo\u00ebl",
      "family": "Janin",
      "sequence": "additional",
      "affiliation": []
    }
  ],
  "member": "311",
  "published-online": {
    "date-parts": [
      [
        2004,
        2,
        3
      ]
    ]
  },
  "reference": [
    {
      "key": "e_1_2_1_2_2",
      "doi-asserted-by": "crossref",
      "first-page": "16027",
      "DOI": "10.1016/S0021-9258(17)46181-3",
      "article-title": "The structure of protein\u2010protein recognition sites",
      "volume": "256",
      "author": "Janin J.",
      "year": "1990",
      "journal-title": "J. Biol. Chem."
    },
    {
      "key": "e_1_2_1_3_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/256705a0"
    },
    {
      "key": "e_1_2_1_4_2",
      "doi-asserted-by": "crossref",
      "first-page": "10541",
      "DOI": "10.1016/S0021-9258(18)38002-5",
      "article-title": "Antibody\u2010antigen complexes",
      "volume": "263",
      "author": "Davies D. R.",
      "year": "1988",
      "journal-title": "J. Biol. Chem."
    },
    {
      "key": "e_1_2_1_5_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1146/annurev.bb.16.060187.001035"
    },
    {
      "key": "e_1_2_1_6_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0022-2836(78)90302-9"
    },
    {
      "key": "e_1_2_1_7_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/bip.360240307"
    },
    {
      "key": "e_1_2_1_8_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0079-6107(87)90008-3"
    },
    {
      "key": "e_1_2_1_9_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0022-2836(76)90004-8"
    },
    {
      "key": "e_1_2_1_10_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.72.4.1330"
    },
    {
      "key": "e_1_2_1_11_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.84.22.8075"
    },
    {
      "key": "e_1_2_1_12_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.86.15.5938"
    },
    {
      "key": "e_1_2_1_13_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.2426778"
    },
    {
      "key": "e_1_2_1_14_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0022-2836(74)90163-6"
    },
    {
      "key": "e_1_2_1_15_2",
      "doi-asserted-by": "crossref",
      "first-page": "813",
      "DOI": "10.1002/j.1460-2075.1986.tb04286.x",
      "article-title": "Refined 1.2 \u00c5 structure of the complex formed between subtilisin Carlsberg and the inhibitor eglin c. Molecular structure of eglin and its detailed interaction with subtilisin",
      "volume": "4",
      "author": "Bode W.",
      "year": "1986",
      "journal-title": "EMBO J"
    },
    {
      "key": "e_1_2_1_16_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/j.1460-2075.1986.tb04521.x"
    },
    {
      "key": "e_1_2_1_17_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0022-2836(77)80200-3"
    },
    {
      "key": "e_1_2_1_18_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0022-2836(73)90011-9"
    },
    {
      "key": "e_1_2_1_19_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0022-2836(71)90324-X"
    },
    {
      "key": "e_1_2_1_20_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.77.4.1736"
    },
    {
      "key": "e_1_2_1_21_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/248338a0"
    },
    {
      "key": "e_1_2_1_22_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.2011744"
    },
    {
      "key": "e_1_2_1_23_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1063/1.1699114"
    },
    {
      "key": "e_1_2_1_24_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.220.4598.671"
    },
    {
      "key": "e_1_2_1_25_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1007/978-94-015-7744-1"
    },
    {
      "key": "e_1_2_1_26_2",
      "volume-title": "X\u2010PLOR Version 1.5 Manual",
      "author": "Br\u00fcnger A.",
      "year": "1987"
    },
    {
      "key": "e_1_2_1_27_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/jcc.540040211"
    },
    {
      "key": "e_1_2_1_28_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0022-2836(74)90598-1"
    },
    {
      "key": "e_1_2_1_29_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1107/S010876818300275X"
    },
    {
      "key": "e_1_2_1_30_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0022-2836(72)90028-9"
    },
    {
      "key": "e_1_2_1_31_2",
      "first-page": "417",
      "article-title": "Structure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor",
      "volume": "77",
      "author": "R\u00fchlmann A.",
      "year": "1973",
      "journal-title": "Crystal structure determination and stereochemistry of the contact region. J. Mol. Biol."
    },
    {
      "key": "e_1_2_1_32_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0022-2836(76)90334-X"
    },
    {
      "key": "e_1_2_1_33_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0022-2836(89)90487-7"
    },
    {
      "key": "e_1_2_1_34_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.75.1.303"
    },
    {
      "key": "e_1_2_1_35_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0022-2836(82)90153-X"
    },
    {
      "key": "e_1_2_1_36_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/bip.360240814"
    },
    {
      "key": "e_1_2_1_37_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/bip.360250705"
    },
    {
      "key": "e_1_2_1_38_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0022-2836(91)90859-5"
    },
    {
      "key": "e_1_2_1_39_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/jm00399a006"
    },
    {
      "key": "e_1_2_1_40_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/319199a0"
    },
    {
      "key": "e_1_2_1_41_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/bi00375a028"
    },
    {
      "key": "e_1_2_1_42_2",
      "doi-asserted-by": "crossref",
      "first-page": "314",
      "DOI": "10.4049/jimmunol.128.1.314",
      "article-title": "Mapping the antigenic epitope for a monoclonal antibody against lysozyme",
      "volume": "128",
      "author": "Smith\u2010Gill S. J.",
      "year": "1982",
      "journal-title": "J. Immunol."
    },
    {
      "key": "e_1_2_1_43_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0161-5890(87)90081-2"
    },
    {
      "key": "e_1_2_1_44_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/314235a0"
    },
    {
      "key": "e_1_2_1_45_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.3810155"
    },
    {
      "key": "e_1_2_1_46_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/bi00437a034"
    },
    {
      "key": "e_1_2_1_47_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/348254a0"
    }
  ],
  "container-title": "Proteins: Structure, Function, and Bioinformatics",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Fprot.340110406",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "text-mining"
    },
    {
      "URL": "https://onlinelibrary.wiley.com/doi/pdf/10.1002/prot.340110406",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2023,
        10,
        23
      ]
    ],
    "date-time": "2023-10-23T07:43:55Z",
    "timestamp": 1698047035000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://onlinelibrary.wiley.com/doi/10.1002/prot.340110406"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        1991,
        12
      ]
    ]
  },
  "references-count": 46,
  "journal-issue": {
    "issue": "4",
    "published-print": {
      "date-parts": [
        [
          1991,
          12
        ]
      ]
    }
  },
  "alternative-id": [
    "10.1002/prot.340110406"
  ],
  "URL": "http://dx.doi.org/10.1002/prot.340110406",
  "relation": {},
  "ISSN": [
    "0887-3585",
    "1097-0134"
  ],
  "subject": [],
  "container-title-short": "Proteins",
  "published": {
    "date-parts": [
      [
        1991,
        12
      ]
    ]
  }
}