DOI: 10.1073/pnas.96.4.1273. Folding pathway of a lattice model for proteins

Folding pathway of a lattice model for proteins

10.1073/pnas.96.4.1273

Crossref journal-article

Proceedings of the National Academy of Sciences

Proceedings of the National Academy of Sciences (341)

Abstract

The folding of a protein-like heteropolymer is studied by using direct simulation of a lattice model that folds rapidly to a well-defined “native” structure. The details of each molecular folding event depend on the random initial conformation as well as the random thermal fluctuations of the polymer. By analyzing the statistical properties of hundreds of folding events, a classical folding “pathway” for such a polymer is found that includes partially folded, on-pathway intermediates that are shown to be metastable equilibrium states of the polymer. These results are discussed in the context of the “classical” and “new” views of folding.

Bibliography

Pande, V. S., & Rokhsar, D. S. (1999). Folding pathway of a lattice model for proteins. Proceedings of the National Academy of Sciences, 96(4), 1273â1278.

Authors 2

Vijay S. Pande (first)
Daniel S. Rokhsar (additional)

References 46 Referenced 99

10.1002/pro.5560050602
10.1111/j.1399-3011.1975.tb02465.x
10.1021/ma00200a030
10.1016/0022-2836(90)90237-G
10.1063/1.468195
10.1038/369248a0
10.1021/bi00199a029
10.1016/S1359-0278(96)00060-0
10.1002/(SICI)1097-0134(19980101)30:1<2::AID-PROT2>3.0.CO;2-R
10.1038/nsb0197-10
10.1016/S0959-440X(98)80012-2
10.1073/pnas.95.11.5921
10.1038/379096a0
D Frenkel, B Smit Understanding Molecular Simulations (Academic, London, 1996). / Understanding Molecular Simulations by Frenkel D (1996)
10.1016/S0959-440X(97)80005-X
D Chandler Introduction to Modern Statistical Mechanics (Oxford Univ. Press, Oxford, 1987). / Introduction to Modern Statistical Mechanics by Chandler D (1987)
10.1073/pnas.76.8.3585
10.1063/1.475393
10.1146/annurev.bi.60.070191.004051
10.1096/fasebj.10.1.8566543
10.1021/bi9627626
10.1016/0959-440X(95)80012-P
10.1016/0014-5793(90)80143-7
10.1126/science.8235610
10.1038/nsb1297-1016
10.1038/nsb0997-725
10.1021/bi971914
10.1063/1.467320
10.1016/S1359-0278(96)00019-3
10.1073/pnas.91.22.10422
10.1073/pnas.92.15.6878
10.1038/nsb0895-663
10.1126/science.7618079
10.1038/nsb0996-782
10.1038/nsb0497-298
10.1002/prot.340060202
10.1016/0959-440X(95)80011-O
10.1016/S0960-9822(00)00141-X
10.1073/pnas.95.4.1490
10.1016/S1359-0278(96)00041-7
10.1006/jmbi.1996.0578
10.1002/pro.5560040615
10.1146/annurev.bi.59.070190.003215
10.1146/annurev.bi.62.070193.003253
10.1073/pnas.92.24.10869
10.1016/S0959-440X(97)80002-4

Dates

Type	When
Created	23 years, 1 month ago (July 26, 2002, 10:42 a.m.)
Deposited	3 years, 4 months ago (April 13, 2022, 5:54 p.m.)
Indexed	1 month, 3 weeks ago (July 11, 2025, 6:24 a.m.)
Issued	26 years, 6 months ago (Feb. 16, 1999)
Published	26 years, 6 months ago (Feb. 16, 1999)
Published Online	26 years, 6 months ago (Feb. 16, 1999)
Published Print	26 years, 6 months ago (Feb. 16, 1999)

Funders 0

None

BibTeX

@article{Pande_1999, title={Folding pathway of a lattice model for proteins}, volume={96}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.96.4.1273}, DOI={10.1073/pnas.96.4.1273}, number={4}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Pande, Vijay S. and Rokhsar, Daniel S.}, year={1999}, month=feb, pages={1273–1278} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        7,
        11
      ]
    ],
    "date-time": "2025-07-11T10:24:37Z",
    "timestamp": 1752229477885
  },
  "reference-count": 46,
  "publisher": "Proceedings of the National Academy of Sciences",
  "issue": "4",
  "content-domain": {
    "domain": [
      "www.pnas.org"
    ],
    "crossmark-restriction": true
  },
  "published-print": {
    "date-parts": [
      [
        1999,
        2,
        16
      ]
    ]
  },
  "abstract": "<jats:p>The folding of a protein-like heteropolymer is studied by using\n direct simulation of a lattice model that folds rapidly to a\n well-defined \u201cnative\u201d structure. The details of each molecular\n folding event depend on the random initial conformation as well as the\n random thermal fluctuations of the polymer. By analyzing the\n statistical properties of hundreds of folding events, a classical\n folding \u201cpathway\u201d for such a polymer is found that includes\n partially folded, on-pathway intermediates that are shown to be\n metastable equilibrium states of the polymer. These results are\n discussed in the context of the \u201cclassical\u201d and \u201cnew\u201d views of\n folding.</jats:p>",
  "DOI": "10.1073/pnas.96.4.1273",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2002,
        7,
        26
      ]
    ],
    "date-time": "2002-07-26T14:42:40Z",
    "timestamp": 1027694560000
  },
  "page": "1273-1278",
  "update-policy": "http://dx.doi.org/10.1073/pnas.cm10313",
  "source": "Crossref",
  "is-referenced-by-count": 99,
  "title": "Folding pathway of a lattice model for proteins",
  "prefix": "10.1073",
  "volume": "96",
  "author": [
    {
      "given": "Vijay S.",
      "family": "Pande",
      "sequence": "first",
      "affiliation": [
        {
          "name": "Physical Biosciences Division, Lawrence Berkeley National\r Laboratory, Berkeley, CA 94720; and Department of Physics,\r University of California at Berkeley, Berkeley, CA 94720-7300"
        }
      ]
    },
    {
      "given": "Daniel S.",
      "family": "Rokhsar",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Physical Biosciences Division, Lawrence Berkeley National\r Laboratory, Berkeley, CA 94720; and Department of Physics,\r University of California at Berkeley, Berkeley, CA 94720-7300"
        }
      ]
    }
  ],
  "member": "341",
  "published-online": {
    "date-parts": [
      [
        1999,
        2,
        16
      ]
    ]
  },
  "reference": [
    {
      "key": "e_1_3_2_1_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/pro.5560050602"
    },
    {
      "key": "e_1_3_2_2_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1111/j.1399-3011.1975.tb02465.x"
    },
    {
      "key": "e_1_3_2_3_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/ma00200a030"
    },
    {
      "key": "e_1_3_2_4_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0022-2836(90)90237-G"
    },
    {
      "key": "e_1_3_2_5_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1063/1.468195"
    },
    {
      "key": "e_1_3_2_6_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/369248a0"
    },
    {
      "key": "e_1_3_2_7_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/bi00199a029"
    },
    {
      "key": "e_1_3_2_8_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S1359-0278(96)00060-0"
    },
    {
      "key": "e_1_3_2_9_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/(SICI)1097-0134(19980101)30:1<2::AID-PROT2>3.0.CO;2-R"
    },
    {
      "key": "e_1_3_2_10_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nsb0197-10"
    },
    {
      "key": "e_1_3_2_11_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0959-440X(98)80012-2"
    },
    {
      "key": "e_1_3_2_12_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.95.11.5921"
    },
    {
      "key": "e_1_3_2_13_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/379096a0"
    },
    {
      "key": "e_1_3_2_14_2",
      "volume-title": "Understanding Molecular Simulations",
      "author": "Frenkel D",
      "year": "1996",
      "unstructured": "D Frenkel, B Smit Understanding Molecular Simulations (Academic, London, 1996)."
    },
    {
      "key": "e_1_3_2_15_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0959-440X(97)80005-X"
    },
    {
      "key": "e_1_3_2_16_2",
      "volume-title": "Introduction to Modern Statistical Mechanics",
      "author": "Chandler D",
      "year": "1987",
      "unstructured": "D Chandler Introduction to Modern Statistical Mechanics (Oxford Univ. Press, Oxford, 1987)."
    },
    {
      "key": "e_1_3_2_17_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.76.8.3585"
    },
    {
      "key": "e_1_3_2_18_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1063/1.475393"
    },
    {
      "key": "e_1_3_2_19_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1146/annurev.bi.60.070191.004051"
    },
    {
      "key": "e_1_3_2_20_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1096/fasebj.10.1.8566543"
    },
    {
      "key": "e_1_3_2_21_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/bi9627626"
    },
    {
      "key": "e_1_3_2_22_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0959-440X(95)80012-P"
    },
    {
      "key": "e_1_3_2_23_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0014-5793(90)80143-7"
    },
    {
      "key": "e_1_3_2_24_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.8235610"
    },
    {
      "key": "e_1_3_2_25_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nsb1297-1016"
    },
    {
      "key": "e_1_3_2_26_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nsb0997-725"
    },
    {
      "key": "e_1_3_2_27_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/bi971914"
    },
    {
      "key": "e_1_3_2_28_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1063/1.467320"
    },
    {
      "key": "e_1_3_2_29_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S1359-0278(96)00019-3"
    },
    {
      "key": "e_1_3_2_30_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.91.22.10422"
    },
    {
      "key": "e_1_3_2_31_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.92.15.6878"
    },
    {
      "key": "e_1_3_2_32_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nsb0895-663"
    },
    {
      "key": "e_1_3_2_33_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.7618079"
    },
    {
      "key": "e_1_3_2_34_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nsb0996-782"
    },
    {
      "key": "e_1_3_2_35_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nsb0497-298"
    },
    {
      "key": "e_1_3_2_36_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/prot.340060202"
    },
    {
      "key": "e_1_3_2_37_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0959-440X(95)80011-O"
    },
    {
      "key": "e_1_3_2_38_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0960-9822(00)00141-X"
    },
    {
      "key": "e_1_3_2_39_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.95.4.1490"
    },
    {
      "key": "e_1_3_2_40_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S1359-0278(96)00041-7"
    },
    {
      "key": "e_1_3_2_41_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/jmbi.1996.0578"
    },
    {
      "key": "e_1_3_2_42_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/pro.5560040615"
    },
    {
      "key": "e_1_3_2_43_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1146/annurev.bi.59.070190.003215"
    },
    {
      "key": "e_1_3_2_44_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1146/annurev.bi.62.070193.003253"
    },
    {
      "key": "e_1_3_2_45_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.92.24.10869"
    },
    {
      "key": "e_1_3_2_46_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0959-440X(97)80002-4"
    }
  ],
  "container-title": "Proceedings of the National Academy of Sciences",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://pnas.org/doi/pdf/10.1073/pnas.96.4.1273",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2022,
        4,
        13
      ]
    ],
    "date-time": "2022-04-13T21:54:31Z",
    "timestamp": 1649886871000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://pnas.org/doi/full/10.1073/pnas.96.4.1273"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        1999,
        2,
        16
      ]
    ]
  },
  "references-count": 46,
  "journal-issue": {
    "issue": "4",
    "published-print": {
      "date-parts": [
        [
          1999,
          2,
          16
        ]
      ]
    }
  },
  "alternative-id": [
    "10.1073/pnas.96.4.1273"
  ],
  "URL": "http://dx.doi.org/10.1073/pnas.96.4.1273",
  "relation": {},
  "ISSN": [
    "0027-8424",
    "1091-6490"
  ],
  "subject": [],
  "container-title-short": "Proc. Natl. Acad. Sci. U.S.A.",
  "published": {
    "date-parts": [
      [
        1999,
        2,
        16
      ]
    ]
  },
  "assertion": [
    {
      "value": "1998-08-14",
      "order": 0,
      "name": "received",
      "label": "Received",
      "group": {
        "name": "publication_history",
        "label": "Publication History"
      }
    },
    {
      "value": "1998-12-02",
      "order": 1,
      "name": "accepted",
      "label": "Accepted",
      "group": {
        "name": "publication_history",
        "label": "Publication History"
      }
    },
    {
      "value": "1999-02-16",
      "order": 2,
      "name": "published",
      "label": "Published",
      "group": {
        "name": "publication_history",
        "label": "Publication History"
      }
    }
  ]
}