DOI: 10.1016/j.jmb.2003.11.033. Heterogeneous Folding of the trpzip Hairpin: Full Atom Simulation and Experiment

Heterogeneous Folding of the trpzip Hairpin: Full Atom Simulation and Experiment

10.1016/j.jmb.2003.11.033

Crossref journal-article

Elsevier BV

Journal of Molecular Biology (78)

Bibliography

Yang, W. Y., Pitera, J. W., Swope, W. C., & Gruebele, M. (2004). Heterogeneous Folding of the trpzip Hairpin: Full Atom Simulation and Experiment. Journal of Molecular Biology, 336(1), 241â251.

Authors 4

Wei Yuan Yang (first)
Jed W. Pitera (additional)
William C. Swope (additional)
Martin Gruebele (additional)

References 45 Referenced 155

10.1016/S1359-0278(98)00033-9 / Fold. Des. / How do small single-domain proteins fold? by Jackson (1998)
10.1038/36626 / Nature / Folding dynamics and mechanism of β-hairpin formation by Muñoz (1997)
10.1073/pnas.97.4.1525 / Proc. Natl Acad. Sci. USA / Transition-state structure as a unifying basis in protein-folding mechanisms: contact order, chain topology, stability, and the extended nucleus mechanism by Fersht (2000)
10.1002/prot.340210302 / Proteins: Struct. Funct. Genet. / Funnels, pathways, and the energy landscape of protein folding: a synthesis by Bryngelson (1995)
10.1021/bi00071a002 / Biochemistry / Structure and stability of an early folding intermediate of Escherichia coli trp aporepressor measured by far-UV stopped-flow circular dichroism and 8-anilino-1-naphthalene sulfonate binding by Mann (1993)
10.1126/science.8235610 / Science / Formation of a molten globule intermediate early in the kinetic folding pathway of apomyoglobin by Jennings (1993)
10.1073/pnas.93.12.5759 / Proc. Natl Acad. Sci. USA / Direct observation of fast protein folding: the initial collapse of apomyoglobin by Ballew (1996)
10.1038/84145 / Nature Struct. Biol. / Structural and kinetic characterization of early folding events in beta-lactoglobulin by Kuwata (2001)
10.1021/jp021433m / J. Phys. Chem. B / Formation of a compact structured ensemble without fluorescence signature early during ubiquitin folding by Qin (2002)
10.1006/jmbi.1999.3204 / J. Mol. Biol. / The cooperativity of burst phase reactions explored by Parker (1999)
10.1073/pnas.96.11.6031 / Proc. Natl Acad. Sci. USA / Observation of strange kinetics in protein folding by Sabelko (1999)
10.1016/j.jmb.2003.08.011 / J. Mol. Biol. / Tuning the heterogeneous early folding dynamics of phosphoglycerate kinase by Osváth (2003)
10.1126/science.1077809 / Science / Experimental identification of downhill protein folding by Garcia-Mira (2002)
10.1038/nature01609 / Nature / Folding at the speed limit by Yang (2003)
10.1038/nature01160 / Nature / Absolute comparison of simulated and experimental protein-folding dynamics by Snow (2002)
10.1021/bi020574b / Biochemistry / Proline cis–trans isomerization and protein folding by Wedemeyer (2002)
{'year': '1970', 'series-title': 'Theory of Helix-Coil Transitions in Biopolymers', 'author': 'Poland', 'key': '10.1016/j.jmb.2003.11.033_BIB17'} / Theory of Helix-Coil Transitions in Biopolymers by Poland (1970)
10.1016/0301-4622(94)00146-B / Biophys. Chem. / α-Helix formation by peptides of defined sequence by Baldwin (1995)
{'key': '10.1016/j.jmb.2003.11.033_BIB19', 'series-title': 'Circular Dichroism and the Conformational Analysis of Biomolecules', 'first-page': '201', 'article-title': 'CD Spectroscopy and the helix-coil transition in peptides and polypeptides', 'author': 'Kallenbach', 'year': '1996'} / Circular Dichroism and the Conformational Analysis of Biomolecules / CD Spectroscopy and the helix-coil transition in peptides and polypeptides by Kallenbach (1996)
10.1021/ja993343+ / J. Am. Chem. Soc. / Transition from exponential to nonexponential kinetics during formation of a nonbiological helix by Yang (2000)
10.1016/0076-6879(84)07021-X / Methods Enzymol. / Disulfide bond formation in proteins by Creighton (1984)
10.1126/science.1749933 / Science / The energy landscapes and motions of proteins by Frauenfelder (1991)
{'key': '10.1016/j.jmb.2003.11.033_BIB23', 'article-title': 'Tryptophan zippers: stable, monomeric beta-hairpins', 'volume': '99', 'author': 'Cochran', 'year': '2002', 'journal-title': 'Proc. Natl Acad. Sci. USA'} / Proc. Natl Acad. Sci. USA / Tryptophan zippers: stable, monomeric beta-hairpins by Cochran (2002)
10.1016/0968-0004(94)90053-1 / Trends Biochem. Sci. / The WW domain: a signalling site in dystrophin? by Bork (1994)
10.1126/science.1067680 / Science / Long-range interactions within a nonnative protein by Klein-Seetharaman (2002)
10.1016/S0162-0134(02)00446-4 / J. Inorg. Biochem. / Thermophilic cytochrome P450 (CYP119) from Sulfolobus solfataricus: high resolution structure and functional properties by Park (2002)
10.1016/S0003-9861(02)00402-2 / Arch. Biochem. Biophys. / Aromatic stacking as a determinant of the thermal stability of CYP119 from Sulfolobus solfataricus by Puchkaev (2003)
10.1016/S0022-2836(02)00888-4 / J. Mol. Biol. / Native-like mean structure in the unfolded ensemble of small proteins by Zagrovic (2002)
10.1073/pnas.091100898 / Proc. Natl Acad. Sci. USA / Tryptophan zippers: stable, monomeric beta-hairpins by Cochran (2001)
10.1039/fd9949900245 / Faraday Discuss. / Contributions of tryptophan side-chains to the circular dichroism of globular proteins: exciton couplets and coupled oscillators by Grishina (1994)
10.1007/BF00213575 / Eur. Biophys. J. / Contributions of tryptophan side-chains to the far-ultraviolet circular dichroism of proteins by Woody (1994)
10.1073/pnas.1330954100 / Proc. Natl Acad. Sci. USA / Understanding folding and design: replica-exchange simulations of “Trp-cage” miniproteins by Pitera (2003)
10.1016/S0006-3495(02)75183-7 / Biophys. J. / What causes hyperfluorescence: folding intermediates or conformationally flexible native states? by Ervin (2002)
10.1038/nsb0497-305 / Nature Struct. Biol. / The energy landscape of a fast-folding protein mapped by Ala→Gly substitutions by Burton (1997)
10.1073/pnas.97.12.6509 / Proc. Natl Acad. Sci. USA / Investigation of routes and funnels in protein folding by free energy functional methods by Plotkin (2000)
10.1110/ps.17601 / Protein Sci. / Understanding thermostability in cytochrome P450 by combinatorial mutagenesis by Maves (2001)
Yang, W. Y., Larios, E., Gruebele, M. (2003). On the beta-structure propensity of polypeptides at high temperature. J. Am. Chem. Soc., in the press.
10.1002/1097-0282(2001)60:2<96::AID-BIP1007>3.0.CO;2-F / Biopolymers / Generalized-ensemble algorithms for molecular simulations of biopolymers by Mitsutake (2001)
10.1051/jcp/1997941417 / J. Chimie Physique Physico-Chimie Biol. / Calculation of the Phi-Psi maps for alanyl and glycyl dipeptides with different additive and non-additive molecular mechanical models by Cornell (1997)
10.1002/1097-0282(2000)56:4<275::AID-BIP10024>3.0.CO;2-E / Biopolymers / Theory and applications of the generalized born solvation model in macromolecular simulations by Tsui (2000)
10.1016/0021-9991(77)90098-5 / J. Comp. Phys. / Numerical-integration of cartesian equations of motion of a system with constraints—molecular-dynamics of N-alkanes by Ryckaert (1977)
{'year': '1999', 'series-title': 'AMBER', 'author': 'Case', 'key': '10.1016/j.jmb.2003.11.033_BIB42'} / AMBER by Case (1999)
10.1063/1.439486 / J. Chem. Phys. / Molecular-dynamics simulations at constant pressure and-or temperature by Andersen (1980)
10.1063/1.448118 / J. Chem. Phys. / Molecular-dynamics with coupling to an external bath by Berendsen (1984)
10.1103/PhysRevLett.63.1195 / Phys. Rev. Letters / Optimized Monte-Carlo data-analysis by Ferrenberg (1989)

Dates

Type	When
Created	21 years, 8 months ago (Dec. 6, 2003, 6:47 a.m.)
Deposited	4 years, 5 months ago (March 25, 2021, 2:14 a.m.)
Indexed	3 weeks, 3 days ago (Aug. 2, 2025, 12:09 a.m.)
Issued	21 years, 6 months ago (Feb. 1, 2004)
Published	21 years, 6 months ago (Feb. 1, 2004)
Published Print	21 years, 6 months ago (Feb. 1, 2004)

Funders 1

National Science Foundation 10.13039/100000001
Region: Americas
gov (National government)
Labels4
1. U.S. National Science Foundation
2. NSF
3. US NSF
4. USA NSF
Awards1
1. MCB-0316925

BibTeX

@article{Yang_2004, title={Heterogeneous Folding of the trpzip Hairpin: Full Atom Simulation and Experiment}, volume={336}, ISSN={0022-2836}, url={http://dx.doi.org/10.1016/j.jmb.2003.11.033}, DOI={10.1016/j.jmb.2003.11.033}, number={1}, journal={Journal of Molecular Biology}, publisher={Elsevier BV}, author={Yang, Wei Yuan and Pitera, Jed W. and Swope, William C. and Gruebele, Martin}, year={2004}, month=feb, pages={241–251} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        8,
        2
      ]
    ],
    "date-time": "2025-08-02T04:09:48Z",
    "timestamp": 1754107788862,
    "version": "3.37.3"
  },
  "reference-count": 45,
  "publisher": "Elsevier BV",
  "issue": "1",
  "license": [
    {
      "start": {
        "date-parts": [
          [
            2004,
            2,
            1
          ]
        ],
        "date-time": "2004-02-01T00:00:00Z",
        "timestamp": 1075593600000
      },
      "content-version": "tdm",
      "delay-in-days": 0,
      "URL": "https://www.elsevier.com/tdm/userlicense/1.0/"
    }
  ],
  "funder": [
    {
      "DOI": "10.13039/100000001",
      "name": "National Science Foundation",
      "doi-asserted-by": "publisher",
      "award": [
        "MCB-0316925"
      ],
      "id": [
        {
          "id": "10.13039/100000001",
          "id-type": "DOI",
          "asserted-by": "publisher"
        }
      ]
    }
  ],
  "content-domain": {
    "domain": [],
    "crossmark-restriction": false
  },
  "published-print": {
    "date-parts": [
      [
        2004,
        2
      ]
    ]
  },
  "DOI": "10.1016/j.jmb.2003.11.033",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2003,
        12,
        6
      ]
    ],
    "date-time": "2003-12-06T11:47:02Z",
    "timestamp": 1070711222000
  },
  "page": "241-251",
  "source": "Crossref",
  "is-referenced-by-count": 155,
  "title": "Heterogeneous Folding of the trpzip Hairpin: Full Atom Simulation and Experiment",
  "prefix": "10.1016",
  "volume": "336",
  "author": [
    {
      "given": "Wei Yuan",
      "family": "Yang",
      "sequence": "first",
      "affiliation": []
    },
    {
      "given": "Jed W.",
      "family": "Pitera",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "William C.",
      "family": "Swope",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Martin",
      "family": "Gruebele",
      "sequence": "additional",
      "affiliation": []
    }
  ],
  "member": "78",
  "reference": [
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB1",
      "doi-asserted-by": "crossref",
      "first-page": "81",
      "DOI": "10.1016/S1359-0278(98)00033-9",
      "article-title": "How do small single-domain proteins fold?",
      "volume": "3",
      "author": "Jackson",
      "year": "1998",
      "journal-title": "Fold. Des."
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB2",
      "doi-asserted-by": "crossref",
      "first-page": "196",
      "DOI": "10.1038/36626",
      "article-title": "Folding dynamics and mechanism of \u03b2-hairpin formation",
      "volume": "390",
      "author": "Mu\u00f1oz",
      "year": "1997",
      "journal-title": "Nature"
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB3",
      "doi-asserted-by": "crossref",
      "first-page": "1525",
      "DOI": "10.1073/pnas.97.4.1525",
      "article-title": "Transition-state structure as a unifying basis in protein-folding mechanisms: contact order, chain topology, stability, and the extended nucleus mechanism",
      "volume": "97",
      "author": "Fersht",
      "year": "2000",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB4",
      "doi-asserted-by": "crossref",
      "first-page": "167",
      "DOI": "10.1002/prot.340210302",
      "article-title": "Funnels, pathways, and the energy landscape of protein folding: a synthesis",
      "volume": "21",
      "author": "Bryngelson",
      "year": "1995",
      "journal-title": "Proteins: Struct. Funct. Genet."
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB5",
      "doi-asserted-by": "crossref",
      "first-page": "5282",
      "DOI": "10.1021/bi00071a002",
      "article-title": "Structure and stability of an early folding intermediate of Escherichia coli trp aporepressor measured by far-UV stopped-flow circular dichroism and 8-anilino-1-naphthalene sulfonate binding",
      "volume": "32",
      "author": "Mann",
      "year": "1993",
      "journal-title": "Biochemistry"
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB6",
      "doi-asserted-by": "crossref",
      "first-page": "892",
      "DOI": "10.1126/science.8235610",
      "article-title": "Formation of a molten globule intermediate early in the kinetic folding pathway of apomyoglobin",
      "volume": "262",
      "author": "Jennings",
      "year": "1993",
      "journal-title": "Science"
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB7",
      "doi-asserted-by": "crossref",
      "first-page": "5759",
      "DOI": "10.1073/pnas.93.12.5759",
      "article-title": "Direct observation of fast protein folding: the initial collapse of apomyoglobin",
      "volume": "93",
      "author": "Ballew",
      "year": "1996",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB8",
      "doi-asserted-by": "crossref",
      "first-page": "151",
      "DOI": "10.1038/84145",
      "article-title": "Structural and kinetic characterization of early folding events in beta-lactoglobulin",
      "volume": "8",
      "author": "Kuwata",
      "year": "2001",
      "journal-title": "Nature Struct. Biol."
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB9",
      "doi-asserted-by": "crossref",
      "first-page": "13040",
      "DOI": "10.1021/jp021433m",
      "article-title": "Formation of a compact structured ensemble without fluorescence signature early during ubiquitin folding",
      "volume": "106",
      "author": "Qin",
      "year": "2002",
      "journal-title": "J. Phys. Chem. B"
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB10",
      "doi-asserted-by": "crossref",
      "first-page": "1195",
      "DOI": "10.1006/jmbi.1999.3204",
      "article-title": "The cooperativity of burst phase reactions explored",
      "volume": "293",
      "author": "Parker",
      "year": "1999",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB11",
      "doi-asserted-by": "crossref",
      "first-page": "6031",
      "DOI": "10.1073/pnas.96.11.6031",
      "article-title": "Observation of strange kinetics in protein folding",
      "volume": "96",
      "author": "Sabelko",
      "year": "1999",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB12",
      "doi-asserted-by": "crossref",
      "first-page": "187",
      "DOI": "10.1016/j.jmb.2003.08.011",
      "article-title": "Tuning the heterogeneous early folding dynamics of phosphoglycerate kinase",
      "volume": "333",
      "author": "Osv\u00e1th",
      "year": "2003",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB13",
      "doi-asserted-by": "crossref",
      "first-page": "2191",
      "DOI": "10.1126/science.1077809",
      "article-title": "Experimental identification of downhill protein folding",
      "volume": "298",
      "author": "Garcia-Mira",
      "year": "2002",
      "journal-title": "Science"
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB14",
      "doi-asserted-by": "crossref",
      "first-page": "193",
      "DOI": "10.1038/nature01609",
      "article-title": "Folding at the speed limit",
      "volume": "423",
      "author": "Yang",
      "year": "2003",
      "journal-title": "Nature"
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB15",
      "doi-asserted-by": "crossref",
      "first-page": "102",
      "DOI": "10.1038/nature01160",
      "article-title": "Absolute comparison of simulated and experimental protein-folding dynamics",
      "volume": "420",
      "author": "Snow",
      "year": "2002",
      "journal-title": "Nature"
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB16",
      "doi-asserted-by": "crossref",
      "first-page": "14637",
      "DOI": "10.1021/bi020574b",
      "article-title": "Proline cis\u2013trans isomerization and protein folding",
      "volume": "41",
      "author": "Wedemeyer",
      "year": "2002",
      "journal-title": "Biochemistry"
    },
    {
      "year": "1970",
      "series-title": "Theory of Helix-Coil Transitions in Biopolymers",
      "author": "Poland",
      "key": "10.1016/j.jmb.2003.11.033_BIB17"
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB18",
      "doi-asserted-by": "crossref",
      "first-page": "127",
      "DOI": "10.1016/0301-4622(94)00146-B",
      "article-title": "\u03b1-Helix formation by peptides of defined sequence",
      "volume": "55",
      "author": "Baldwin",
      "year": "1995",
      "journal-title": "Biophys. Chem."
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB19",
      "series-title": "Circular Dichroism and the Conformational Analysis of Biomolecules",
      "first-page": "201",
      "article-title": "CD Spectroscopy and the helix-coil transition in peptides and polypeptides",
      "author": "Kallenbach",
      "year": "1996"
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB20",
      "doi-asserted-by": "crossref",
      "first-page": "3248",
      "DOI": "10.1021/ja993343+",
      "article-title": "Transition from exponential to nonexponential kinetics during formation of a nonbiological helix",
      "volume": "122",
      "author": "Yang",
      "year": "2000",
      "journal-title": "J. Am. Chem. Soc."
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB21",
      "doi-asserted-by": "crossref",
      "first-page": "305",
      "DOI": "10.1016/0076-6879(84)07021-X",
      "article-title": "Disulfide bond formation in proteins",
      "volume": "107",
      "author": "Creighton",
      "year": "1984",
      "journal-title": "Methods Enzymol."
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB22",
      "doi-asserted-by": "crossref",
      "first-page": "1598",
      "DOI": "10.1126/science.1749933",
      "article-title": "The energy landscapes and motions of proteins",
      "volume": "254",
      "author": "Frauenfelder",
      "year": "1991",
      "journal-title": "Science"
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB23",
      "article-title": "Tryptophan zippers: stable, monomeric beta-hairpins",
      "volume": "99",
      "author": "Cochran",
      "year": "2002",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB24",
      "doi-asserted-by": "crossref",
      "first-page": "531",
      "DOI": "10.1016/0968-0004(94)90053-1",
      "article-title": "The WW domain: a signalling site in dystrophin?",
      "volume": "19",
      "author": "Bork",
      "year": "1994",
      "journal-title": "Trends Biochem. Sci."
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB25",
      "doi-asserted-by": "crossref",
      "first-page": "1719",
      "DOI": "10.1126/science.1067680",
      "article-title": "Long-range interactions within a nonnative protein",
      "volume": "295",
      "author": "Klein-Seetharaman",
      "year": "2002",
      "journal-title": "Science"
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB26",
      "doi-asserted-by": "crossref",
      "first-page": "491",
      "DOI": "10.1016/S0162-0134(02)00446-4",
      "article-title": "Thermophilic cytochrome P450 (CYP119) from Sulfolobus solfataricus: high resolution structure and functional properties",
      "volume": "91",
      "author": "Park",
      "year": "2002",
      "journal-title": "J. Inorg. Biochem."
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB27",
      "doi-asserted-by": "crossref",
      "first-page": "52",
      "DOI": "10.1016/S0003-9861(02)00402-2",
      "article-title": "Aromatic stacking as a determinant of the thermal stability of CYP119 from Sulfolobus solfataricus",
      "volume": "409",
      "author": "Puchkaev",
      "year": "2003",
      "journal-title": "Arch. Biochem. Biophys."
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB28",
      "doi-asserted-by": "crossref",
      "first-page": "153",
      "DOI": "10.1016/S0022-2836(02)00888-4",
      "article-title": "Native-like mean structure in the unfolded ensemble of small proteins",
      "volume": "323",
      "author": "Zagrovic",
      "year": "2002",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB29",
      "doi-asserted-by": "crossref",
      "first-page": "5578",
      "DOI": "10.1073/pnas.091100898",
      "article-title": "Tryptophan zippers: stable, monomeric beta-hairpins",
      "volume": "98",
      "author": "Cochran",
      "year": "2001",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB30",
      "doi-asserted-by": "crossref",
      "first-page": "245",
      "DOI": "10.1039/fd9949900245",
      "article-title": "Contributions of tryptophan side-chains to the circular dichroism of globular proteins: exciton couplets and coupled oscillators",
      "volume": "99",
      "author": "Grishina",
      "year": "1994",
      "journal-title": "Faraday Discuss."
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB31",
      "doi-asserted-by": "crossref",
      "first-page": "253",
      "DOI": "10.1007/BF00213575",
      "article-title": "Contributions of tryptophan side-chains to the far-ultraviolet circular dichroism of proteins",
      "volume": "23",
      "author": "Woody",
      "year": "1994",
      "journal-title": "Eur. Biophys. J."
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB32",
      "doi-asserted-by": "crossref",
      "first-page": "7587",
      "DOI": "10.1073/pnas.1330954100",
      "article-title": "Understanding folding and design: replica-exchange simulations of \u201cTrp-cage\u201d miniproteins",
      "volume": "100",
      "author": "Pitera",
      "year": "2003",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB33",
      "doi-asserted-by": "crossref",
      "first-page": "473",
      "DOI": "10.1016/S0006-3495(02)75183-7",
      "article-title": "What causes hyperfluorescence: folding intermediates or conformationally flexible native states?",
      "volume": "83",
      "author": "Ervin",
      "year": "2002",
      "journal-title": "Biophys. J."
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB34",
      "doi-asserted-by": "crossref",
      "first-page": "305",
      "DOI": "10.1038/nsb0497-305",
      "article-title": "The energy landscape of a fast-folding protein mapped by Ala\u2192Gly substitutions",
      "volume": "4",
      "author": "Burton",
      "year": "1997",
      "journal-title": "Nature Struct. Biol."
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB35",
      "doi-asserted-by": "crossref",
      "first-page": "6509",
      "DOI": "10.1073/pnas.97.12.6509",
      "article-title": "Investigation of routes and funnels in protein folding by free energy functional methods",
      "volume": "97",
      "author": "Plotkin",
      "year": "2000",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB36",
      "doi-asserted-by": "crossref",
      "first-page": "161",
      "DOI": "10.1110/ps.17601",
      "article-title": "Understanding thermostability in cytochrome P450 by combinatorial mutagenesis",
      "volume": "10",
      "author": "Maves",
      "year": "2001",
      "journal-title": "Protein Sci."
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB37",
      "unstructured": "Yang, W. Y., Larios, E., Gruebele, M. (2003). On the beta-structure propensity of polypeptides at high temperature. J. Am. Chem. Soc., in the press."
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB38",
      "doi-asserted-by": "crossref",
      "first-page": "96",
      "DOI": "10.1002/1097-0282(2001)60:2<96::AID-BIP1007>3.0.CO;2-F",
      "article-title": "Generalized-ensemble algorithms for molecular simulations of biopolymers",
      "volume": "60",
      "author": "Mitsutake",
      "year": "2001",
      "journal-title": "Biopolymers"
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB39",
      "doi-asserted-by": "crossref",
      "first-page": "1417",
      "DOI": "10.1051/jcp/1997941417",
      "article-title": "Calculation of the Phi-Psi maps for alanyl and glycyl dipeptides with different additive and non-additive molecular mechanical models",
      "volume": "94",
      "author": "Cornell",
      "year": "1997",
      "journal-title": "J. Chimie Physique Physico-Chimie Biol."
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB40",
      "doi-asserted-by": "crossref",
      "first-page": "275",
      "DOI": "10.1002/1097-0282(2000)56:4<275::AID-BIP10024>3.0.CO;2-E",
      "article-title": "Theory and applications of the generalized born solvation model in macromolecular simulations",
      "volume": "56",
      "author": "Tsui",
      "year": "2000",
      "journal-title": "Biopolymers"
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB41",
      "doi-asserted-by": "crossref",
      "first-page": "327",
      "DOI": "10.1016/0021-9991(77)90098-5",
      "article-title": "Numerical-integration of cartesian equations of motion of a system with constraints\u2014molecular-dynamics of N-alkanes",
      "volume": "23",
      "author": "Ryckaert",
      "year": "1977",
      "journal-title": "J. Comp. Phys."
    },
    {
      "year": "1999",
      "series-title": "AMBER",
      "author": "Case",
      "key": "10.1016/j.jmb.2003.11.033_BIB42"
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB43",
      "doi-asserted-by": "crossref",
      "first-page": "2384",
      "DOI": "10.1063/1.439486",
      "article-title": "Molecular-dynamics simulations at constant pressure and-or temperature",
      "volume": "72",
      "author": "Andersen",
      "year": "1980",
      "journal-title": "J. Chem. Phys."
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB44",
      "doi-asserted-by": "crossref",
      "first-page": "3684",
      "DOI": "10.1063/1.448118",
      "article-title": "Molecular-dynamics with coupling to an external bath",
      "volume": "81",
      "author": "Berendsen",
      "year": "1984",
      "journal-title": "J. Chem. Phys."
    },
    {
      "key": "10.1016/j.jmb.2003.11.033_BIB45",
      "doi-asserted-by": "crossref",
      "first-page": "1195",
      "DOI": "10.1103/PhysRevLett.63.1195",
      "article-title": "Optimized Monte-Carlo data-analysis",
      "volume": "63",
      "author": "Ferrenberg",
      "year": "1989",
      "journal-title": "Phys. Rev. Letters"
    }
  ],
  "container-title": "Journal of Molecular Biology",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://api.elsevier.com/content/article/PII:S0022283603014451?httpAccept=text/xml",
      "content-type": "text/xml",
      "content-version": "vor",
      "intended-application": "text-mining"
    },
    {
      "URL": "https://api.elsevier.com/content/article/PII:S0022283603014451?httpAccept=text/plain",
      "content-type": "text/plain",
      "content-version": "vor",
      "intended-application": "text-mining"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2021,
        3,
        25
      ]
    ],
    "date-time": "2021-03-25T06:14:26Z",
    "timestamp": 1616652866000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://linkinghub.elsevier.com/retrieve/pii/S0022283603014451"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2004,
        2
      ]
    ]
  },
  "references-count": 45,
  "journal-issue": {
    "issue": "1",
    "published-print": {
      "date-parts": [
        [
          2004,
          2
        ]
      ]
    }
  },
  "alternative-id": [
    "S0022283603014451"
  ],
  "URL": "http://dx.doi.org/10.1016/j.jmb.2003.11.033",
  "relation": {},
  "ISSN": [
    "0022-2836"
  ],
  "subject": [],
  "container-title-short": "Journal of Molecular Biology",
  "published": {
    "date-parts": [
      [
        2004,
        2
      ]
    ]
  }
}