DOI: 10.1371/journal.pone.0066065. Fitness Costs of Mutations at the HIV-1 Capsid Hexamerization Interface

Fitness Costs of Mutations at the HIV-1 Capsid Hexamerization Interface

10.1371/journal.pone.0066065

Crossref journal-article

Public Library of Science (PLoS)

PLoS ONE (340)

Bibliography

Manocheewa, S., Swain, J. V., Lanxon-Cookson, E., Rolland, M., & Mullins, J. I. (2013). Fitness Costs of Mutations at the HIV-1 Capsid Hexamerization Interface. PLoS ONE, 8(6), e66065.

Authors 5

Siriphan Manocheewa (first)
J. Victor Swain (additional)
Erinn Lanxon-Cookson (additional)
Morgane Rolland (additional)
James I. Mullins (additional)

References 33 Referenced 28

10.1016/j.sbi.2008.02.001 / Curr Opin Struct Biol / The structural biology of HIV assembly by BK Ganser-Pornillos (2008)
10.1126/science.283.5398.80 / Science / Assembly and analysis of conical models for the HIV-1 core by BK Ganser (1999)
10.1093/emboj/cdg143 / EMBO J / Structural organization of authentic, mature HIV-1 virions and cores by JA Briggs (2003)
10.1093/emboj/18.5.1124 / EMBO J / Head-to-tail dimers and interdomain flexibility revealed by the crystal structure of HIV-1 capsid protein (p24) complexed with a monoclonal antibody Fab by C Berthet-Colominas (1999)
10.1016/j.cell.2009.04.063 / Cell / X-ray structures of the hexameric building block of the HIV capsid by O Pornillos (2009)
10.1128/JVI.76.11.5667-5677.2002 / J Virol / Formation of a human immunodeficiency virus type 1 core of optimal stability is crucial for viral replication by BM Forshey (2002)
10.1128/JVI.77.9.5439-5450.2003 / J Virol / Functional surfaces of the human immunodeficiency virus type 1 capsid protein by UK von Schwedler (2003)
10.1074/jbc.M804230200 / J Biol Chem / Residues in the HIV-1 capsid assembly inhibitor binding site are essential for maintaining the assembly-competent quaternary structure of the capsid protein by V Bartonova (2008)
10.1128/JVI.75.19.9357-9366.2001 / J Virol / Human immunodeficiency virus type 1 N-terminal capsid mutants that exhibit aberrant core morphology and are blocked in initiation of reverse transcription in infected cells by S Tang (2001)
Bocanegra R, Rodriguez-Huete A, Fuertes MA, Del Alamo M, Mateu MG (2012) Molecular recognition in the human immunodeficiency virus capsid and antiviral design. Virus Res. (10.1016/j.virusres.2012.06.016)
10.1128/JVI.68.7.4650-4655.1994 / J Virol / Temporal association of cellular immune responses with the initial control of viremia in primary human immunodeficiency virus type 1 syndrome by RA Koup (1994)
10.1038/nm1520 / Nat Med / CD8+ T-cell responses to different HIV proteins have discordant associations with viral load by P Kiepiela (2007)
10.1128/JVI.00575-06 / J Virol / Selection on the human immunodeficiency virus type 1 proteome following primary infection by Y Liu (2006)
10.1128/JVI.79.21.13239-13249.2005 / J Virol / Selective escape from CD8+ T-cell responses represents a major driving force of human immunodeficiency virus type 1 (HIV-1) sequence diversity and reveals constraints on HIV-1 evolution by TM Allen (2005)
10.1371/journal.ppat.0030157 / PLoS Pathogens / HIV-1 Group M Conserved Elements Vaccine by M Rolland (2007)
10.1371/journal.pone.0029717 / PLoS ONE / CTL responses of high functional avidity and broad variant cross-reactivity are associated with HIV control by B Mothe (2012)
10.1093/nar/gkn860 / Nucleic Acids Res / PDBsum new things by RA Laskowski (2009)
Maddison WP, Maddison DR (2011) Mesquite: a modular system for evolutionary analysis. 2.75 ed.
Nickle DC, Jensen MA, Gottlieb GS, Shriner D, Learn GH, et al.. (2003) Consensus and ancestral state HIV vaccines. Science 299: 1515–1518; author reply 1515–1518. (10.1126/science.299.5612.1515c)
10.2144/000113370 / Biotechniques / DIVEIN: A Web Server to Analyze Phylogenies, Sequence Divergence, Diversity, and Informative Sites by W Deng (2010)
10.1097/QAI.0b013e318030f5c5 / J Acquir Immune Defic Syndr / Granulocyte-monocyte colony-stimulating factor upregulates HIV-1 replication in monocyte-derived macrophages cultured at low density by J McClure (2007)
{'key': 'ref22', 'first-page': '493', 'article-title': 'A simple method of estimating fifty percent endpoints', 'volume': '27', 'author': 'LJ Reed', 'year': '1938', 'journal-title': 'Am J Hyg'} / Am J Hyg / A simple method of estimating fifty percent endpoints by LJ Reed (1938)
10.1371/journal.ppat.1000365 / PLoS Pathog / Variable fitness impact of HIV-1 escape mutations to cytotoxic T lymphocyte (CTL) response by RM Troyer (2009)
Liu Y, Mullins JI, etal (2012) A sensitive real-time PCR based assay to estimate the impact of amino acid substitutions on the competitive replication fitness of human immunodeficiency virus type 1 in cell culture. Journal of Virological Methods: In Press. (10.1016/j.jviromet.2012.10.016)
10.1186/1471-2105-11-261 / BMC Bioinformatics / vFitness: a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments by J Ma (2010)
10.1128/JVI.80.5.2380-2389.2006 / J Virol / Modeling and estimation of replication fitness of human immunodeficiency virus type 1 in vitro experiments by using a growth competition assay by H Wu (2006)
10.1128/JVI.02683-06 / J Virol / Reconstruction and function of ancestral center-of-tree human immunodeficiency virus type 1 proteins by M Rolland (2007)
10.1371/journal.pcbi.1000225 / PLoS Comput Biol / Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag by JM Carlson (2008)
10.1038/nature09640 / Nature / Atomic-level modelling of the HIV capsid by O Pornillos (2011)
10.1016/j.jmb.2012.01.014 / J Mol Biol / A structural model for the generation of continuous curvature on the surface of a retroviral capsid by GD Bailey (2012)
Rolland M, Manocheewa S, Swain JV, Lanxon-Cookson EC, Kim M, et al.. (2013) HIV-1 conserved elements vaccines: Relationship between sequence conservation and replicative capacity. J Virol. (10.1128/JVI.03033-12)
10.1186/1479-5876-9-208 / J Transl Med / Definition of the viral targets of protective HIV-1-specific T cell responses by B Mothe (2011)
10.1016/j.vaccine.2010.12.131 / Vaccine / Preclinical evaluation of HIV-1 therapeutic ex vivo dendritic cell vaccines expressing consensus Gag antigens and conserved Gag epitopes by L Niu (2011)

Dates

Type	When
Created	12 years, 2 months ago (June 13, 2013, 5:11 p.m.)
Deposited	5 years, 1 month ago (July 28, 2020, 6:52 a.m.)
Indexed	2 months, 3 weeks ago (June 8, 2025, 2:22 p.m.)
Issued	12 years, 2 months ago (June 13, 2013)
Published	12 years, 2 months ago (June 13, 2013)
Published Online	12 years, 2 months ago (June 13, 2013)

Funders 0

None

BibTeX

@article{Manocheewa_2013, title={Fitness Costs of Mutations at the HIV-1 Capsid Hexamerization Interface}, volume={8}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0066065}, DOI={10.1371/journal.pone.0066065}, number={6}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Manocheewa, Siriphan and Swain, J. Victor and Lanxon-Cookson, Erinn and Rolland, Morgane and Mullins, James I.}, editor={Barbour, Jason D.}, year={2013}, month=jun, pages={e66065} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        6,
        8
      ]
    ],
    "date-time": "2025-06-08T18:22:37Z",
    "timestamp": 1749406957288
  },
  "reference-count": 33,
  "publisher": "Public Library of Science (PLoS)",
  "issue": "6",
  "license": [
    {
      "start": {
        "date-parts": [
          [
            2013,
            6,
            13
          ]
        ],
        "date-time": "2013-06-13T00:00:00Z",
        "timestamp": 1371081600000
      },
      "content-version": "unspecified",
      "delay-in-days": 0,
      "URL": "http://creativecommons.org/licenses/by/4.0/"
    }
  ],
  "content-domain": {
    "domain": [
      "www.plosone.org"
    ],
    "crossmark-restriction": false
  },
  "DOI": "10.1371/journal.pone.0066065",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2013,
        6,
        13
      ]
    ],
    "date-time": "2013-06-13T21:11:32Z",
    "timestamp": 1371157892000
  },
  "page": "e66065",
  "update-policy": "http://dx.doi.org/10.1371/journal.pone.corrections_policy",
  "source": "Crossref",
  "is-referenced-by-count": 28,
  "title": "Fitness Costs of Mutations at the HIV-1 Capsid Hexamerization Interface",
  "prefix": "10.1371",
  "volume": "8",
  "author": [
    {
      "given": "Siriphan",
      "family": "Manocheewa",
      "sequence": "first",
      "affiliation": []
    },
    {
      "given": "J. Victor",
      "family": "Swain",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Erinn",
      "family": "Lanxon-Cookson",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Morgane",
      "family": "Rolland",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "James I.",
      "family": "Mullins",
      "sequence": "additional",
      "affiliation": []
    }
  ],
  "member": "340",
  "published-online": {
    "date-parts": [
      [
        2013,
        6,
        13
      ]
    ]
  },
  "reference": [
    {
      "key": "ref1",
      "doi-asserted-by": "crossref",
      "first-page": "203",
      "DOI": "10.1016/j.sbi.2008.02.001",
      "article-title": "The structural biology of HIV assembly",
      "volume": "18",
      "author": "BK Ganser-Pornillos",
      "year": "2008",
      "journal-title": "Curr Opin Struct Biol"
    },
    {
      "key": "ref2",
      "doi-asserted-by": "crossref",
      "first-page": "80",
      "DOI": "10.1126/science.283.5398.80",
      "article-title": "Assembly and analysis of conical models for the HIV-1 core",
      "volume": "283",
      "author": "BK Ganser",
      "year": "1999",
      "journal-title": "Science"
    },
    {
      "key": "ref3",
      "doi-asserted-by": "crossref",
      "first-page": "1707",
      "DOI": "10.1093/emboj/cdg143",
      "article-title": "Structural organization of authentic, mature HIV-1 virions and cores",
      "volume": "22",
      "author": "JA Briggs",
      "year": "2003",
      "journal-title": "EMBO J"
    },
    {
      "key": "ref4",
      "doi-asserted-by": "crossref",
      "first-page": "1124",
      "DOI": "10.1093/emboj/18.5.1124",
      "article-title": "Head-to-tail dimers and interdomain flexibility revealed by the crystal structure of HIV-1 capsid protein (p24) complexed with a monoclonal antibody Fab",
      "volume": "18",
      "author": "C Berthet-Colominas",
      "year": "1999",
      "journal-title": "EMBO J"
    },
    {
      "key": "ref5",
      "doi-asserted-by": "crossref",
      "first-page": "1282",
      "DOI": "10.1016/j.cell.2009.04.063",
      "article-title": "X-ray structures of the hexameric building block of the HIV capsid",
      "volume": "137",
      "author": "O Pornillos",
      "year": "2009",
      "journal-title": "Cell"
    },
    {
      "key": "ref6",
      "doi-asserted-by": "crossref",
      "first-page": "5667",
      "DOI": "10.1128/JVI.76.11.5667-5677.2002",
      "article-title": "Formation of a human immunodeficiency virus type 1 core of optimal stability is crucial for viral replication",
      "volume": "76",
      "author": "BM Forshey",
      "year": "2002",
      "journal-title": "J Virol"
    },
    {
      "key": "ref7",
      "doi-asserted-by": "crossref",
      "first-page": "5439",
      "DOI": "10.1128/JVI.77.9.5439-5450.2003",
      "article-title": "Functional surfaces of the human immunodeficiency virus type 1 capsid protein",
      "volume": "77",
      "author": "UK von Schwedler",
      "year": "2003",
      "journal-title": "J Virol"
    },
    {
      "key": "ref8",
      "doi-asserted-by": "crossref",
      "first-page": "32024",
      "DOI": "10.1074/jbc.M804230200",
      "article-title": "Residues in the HIV-1 capsid assembly inhibitor binding site are essential for maintaining the assembly-competent quaternary structure of the capsid protein",
      "volume": "283",
      "author": "V Bartonova",
      "year": "2008",
      "journal-title": "J Biol Chem"
    },
    {
      "key": "ref9",
      "doi-asserted-by": "crossref",
      "first-page": "9357",
      "DOI": "10.1128/JVI.75.19.9357-9366.2001",
      "article-title": "Human immunodeficiency virus type 1 N-terminal capsid mutants that exhibit aberrant core morphology and are blocked in initiation of reverse transcription in infected cells",
      "volume": "75",
      "author": "S Tang",
      "year": "2001",
      "journal-title": "J Virol"
    },
    {
      "key": "ref10",
      "doi-asserted-by": "crossref",
      "unstructured": "Bocanegra R, Rodriguez-Huete A, Fuertes MA, Del Alamo M, Mateu MG (2012) Molecular recognition in the human immunodeficiency virus capsid and antiviral design. Virus Res.",
      "DOI": "10.1016/j.virusres.2012.06.016"
    },
    {
      "key": "ref11",
      "doi-asserted-by": "crossref",
      "first-page": "4650",
      "DOI": "10.1128/JVI.68.7.4650-4655.1994",
      "article-title": "Temporal association of cellular immune responses with the initial control of viremia in primary human immunodeficiency virus type 1 syndrome",
      "volume": "68",
      "author": "RA Koup",
      "year": "1994",
      "journal-title": "J Virol"
    },
    {
      "key": "ref12",
      "doi-asserted-by": "crossref",
      "first-page": "46",
      "DOI": "10.1038/nm1520",
      "article-title": "CD8+ T-cell responses to different HIV proteins have discordant associations with viral load",
      "volume": "13",
      "author": "P Kiepiela",
      "year": "2007",
      "journal-title": "Nat Med"
    },
    {
      "key": "ref13",
      "doi-asserted-by": "crossref",
      "first-page": "9519",
      "DOI": "10.1128/JVI.00575-06",
      "article-title": "Selection on the human immunodeficiency virus type 1 proteome following primary infection",
      "volume": "80",
      "author": "Y Liu",
      "year": "2006",
      "journal-title": "J Virol"
    },
    {
      "key": "ref14",
      "doi-asserted-by": "crossref",
      "first-page": "13239",
      "DOI": "10.1128/JVI.79.21.13239-13249.2005",
      "article-title": "Selective escape from CD8+ T-cell responses represents a major driving force of human immunodeficiency virus type 1 (HIV-1) sequence diversity and reveals constraints on HIV-1 evolution",
      "volume": "79",
      "author": "TM Allen",
      "year": "2005",
      "journal-title": "J Virol"
    },
    {
      "key": "ref15",
      "doi-asserted-by": "crossref",
      "first-page": "e157",
      "DOI": "10.1371/journal.ppat.0030157",
      "article-title": "HIV-1 Group M Conserved Elements Vaccine",
      "volume": "3",
      "author": "M Rolland",
      "year": "2007",
      "journal-title": "PLoS Pathogens"
    },
    {
      "key": "ref16",
      "doi-asserted-by": "crossref",
      "first-page": "e29717",
      "DOI": "10.1371/journal.pone.0029717",
      "article-title": "CTL responses of high functional avidity and broad variant cross-reactivity are associated with HIV control",
      "volume": "7",
      "author": "B Mothe",
      "year": "2012",
      "journal-title": "PLoS ONE"
    },
    {
      "key": "ref17",
      "doi-asserted-by": "crossref",
      "first-page": "D355",
      "DOI": "10.1093/nar/gkn860",
      "article-title": "PDBsum new things",
      "volume": "37",
      "author": "RA Laskowski",
      "year": "2009",
      "journal-title": "Nucleic Acids Res"
    },
    {
      "key": "ref18",
      "unstructured": "Maddison WP, Maddison DR (2011) Mesquite: a modular system for evolutionary analysis. 2.75 ed."
    },
    {
      "key": "ref19",
      "doi-asserted-by": "crossref",
      "unstructured": "Nickle DC, Jensen MA, Gottlieb GS, Shriner D, Learn GH, et al.. (2003) Consensus and ancestral state HIV vaccines. Science 299: 1515\u20131518; author reply 1515\u20131518.",
      "DOI": "10.1126/science.299.5612.1515c"
    },
    {
      "key": "ref20",
      "doi-asserted-by": "crossref",
      "first-page": "405",
      "DOI": "10.2144/000113370",
      "article-title": "DIVEIN: A Web Server to Analyze Phylogenies, Sequence Divergence, Diversity, and Informative Sites",
      "volume": "48",
      "author": "W Deng",
      "year": "2010",
      "journal-title": "Biotechniques"
    },
    {
      "key": "ref21",
      "doi-asserted-by": "crossref",
      "first-page": "254",
      "DOI": "10.1097/QAI.0b013e318030f5c5",
      "article-title": "Granulocyte-monocyte colony-stimulating factor upregulates HIV-1 replication in monocyte-derived macrophages cultured at low density",
      "volume": "44",
      "author": "J McClure",
      "year": "2007",
      "journal-title": "J Acquir Immune Defic Syndr"
    },
    {
      "key": "ref22",
      "first-page": "493",
      "article-title": "A simple method of estimating fifty percent endpoints",
      "volume": "27",
      "author": "LJ Reed",
      "year": "1938",
      "journal-title": "Am J Hyg"
    },
    {
      "key": "ref23",
      "doi-asserted-by": "crossref",
      "first-page": "e1000365",
      "DOI": "10.1371/journal.ppat.1000365",
      "article-title": "Variable fitness impact of HIV-1 escape mutations to cytotoxic T lymphocyte (CTL) response",
      "volume": "5",
      "author": "RM Troyer",
      "year": "2009",
      "journal-title": "PLoS Pathog"
    },
    {
      "key": "ref24",
      "doi-asserted-by": "crossref",
      "unstructured": "Liu Y, Mullins JI, etal (2012) A sensitive real-time PCR based assay to estimate the impact of amino acid substitutions on the competitive replication fitness of human immunodeficiency virus type 1 in cell culture. Journal of Virological Methods: In Press.",
      "DOI": "10.1016/j.jviromet.2012.10.016"
    },
    {
      "key": "ref25",
      "doi-asserted-by": "crossref",
      "first-page": "261",
      "DOI": "10.1186/1471-2105-11-261",
      "article-title": "vFitness: a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments",
      "volume": "11",
      "author": "J Ma",
      "year": "2010",
      "journal-title": "BMC Bioinformatics"
    },
    {
      "key": "ref26",
      "doi-asserted-by": "crossref",
      "first-page": "2380",
      "DOI": "10.1128/JVI.80.5.2380-2389.2006",
      "article-title": "Modeling and estimation of replication fitness of human immunodeficiency virus type 1 in vitro experiments by using a growth competition assay",
      "volume": "80",
      "author": "H Wu",
      "year": "2006",
      "journal-title": "J Virol"
    },
    {
      "key": "ref27",
      "doi-asserted-by": "crossref",
      "first-page": "8507",
      "DOI": "10.1128/JVI.02683-06",
      "article-title": "Reconstruction and function of ancestral center-of-tree human immunodeficiency virus type 1 proteins",
      "volume": "81",
      "author": "M Rolland",
      "year": "2007",
      "journal-title": "J Virol"
    },
    {
      "key": "ref28",
      "doi-asserted-by": "crossref",
      "first-page": "e1000225",
      "DOI": "10.1371/journal.pcbi.1000225",
      "article-title": "Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag",
      "volume": "4",
      "author": "JM Carlson",
      "year": "2008",
      "journal-title": "PLoS Comput Biol"
    },
    {
      "key": "ref29",
      "doi-asserted-by": "crossref",
      "first-page": "424",
      "DOI": "10.1038/nature09640",
      "article-title": "Atomic-level modelling of the HIV capsid",
      "volume": "469",
      "author": "O Pornillos",
      "year": "2011",
      "journal-title": "Nature"
    },
    {
      "key": "ref30",
      "doi-asserted-by": "crossref",
      "first-page": "212",
      "DOI": "10.1016/j.jmb.2012.01.014",
      "article-title": "A structural model for the generation of continuous curvature on the surface of a retroviral capsid",
      "volume": "417",
      "author": "GD Bailey",
      "year": "2012",
      "journal-title": "J Mol Biol"
    },
    {
      "key": "ref31",
      "doi-asserted-by": "crossref",
      "unstructured": "Rolland M, Manocheewa S, Swain JV, Lanxon-Cookson EC, Kim M, et al.. (2013) HIV-1 conserved elements vaccines: Relationship between sequence conservation and replicative capacity. J Virol.",
      "DOI": "10.1128/JVI.03033-12"
    },
    {
      "key": "ref32",
      "doi-asserted-by": "crossref",
      "first-page": "208",
      "DOI": "10.1186/1479-5876-9-208",
      "article-title": "Definition of the viral targets of protective HIV-1-specific T cell responses",
      "volume": "9",
      "author": "B Mothe",
      "year": "2011",
      "journal-title": "J Transl Med"
    },
    {
      "key": "ref33",
      "doi-asserted-by": "crossref",
      "first-page": "2110",
      "DOI": "10.1016/j.vaccine.2010.12.131",
      "article-title": "Preclinical evaluation of HIV-1 therapeutic ex vivo dendritic cell vaccines expressing consensus Gag antigens and conserved Gag epitopes",
      "volume": "29",
      "author": "L Niu",
      "year": "2011",
      "journal-title": "Vaccine"
    }
  ],
  "container-title": "PLoS ONE",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "http://dx.plos.org/10.1371/journal.pone.0066065",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2020,
        7,
        28
      ]
    ],
    "date-time": "2020-07-28T10:52:05Z",
    "timestamp": 1595933525000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://dx.plos.org/10.1371/journal.pone.0066065"
    }
  },
  "subtitle": [],
  "editor": [
    {
      "given": "Jason D.",
      "family": "Barbour",
      "sequence": "first",
      "affiliation": []
    }
  ],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2013,
        6,
        13
      ]
    ]
  },
  "references-count": 33,
  "journal-issue": {
    "issue": "6",
    "published-online": {
      "date-parts": [
        [
          2013,
          6,
          13
        ]
      ]
    }
  },
  "URL": "http://dx.doi.org/10.1371/journal.pone.0066065",
  "relation": {},
  "ISSN": [
    "1932-6203"
  ],
  "subject": [],
  "container-title-short": "PLoS ONE",
  "published": {
    "date-parts": [
      [
        2013,
        6,
        13
      ]
    ]
  }
}