A test of lattice protein folding algorithms.
Identifieur interne : 004059 ( Main/Exploration ); précédent : 004058; suivant : 004060A test of lattice protein folding algorithms.
Auteurs : K. Yue ; K M Fiebig ; P D Thomas ; H S Chan ; E I Shakhnovich ; K A DillSource :
- Proceedings of the National Academy of Sciences of the United States of America [ 0027-8424 ] ; 1995.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Proteins.
- Algorithms, Amino Acid Sequence, Humans, Models, Molecular, Molecular Sequence Data, Protein Conformation, Protein Folding, Reproducibility of Results.
Abstract
We report a blind test of lattice-model-based search strategies for finding global minima of model protein chains. One of us (E.I.S.) selected 10 compact conformations of 48-mer chains on the three-dimensional cubic lattice and used their inverse folding algorithm to design HP (H, hydrophobic; P, polar) sequences that should fold to those "target" structures. The sequences, but not the structures, were sent to the UCSF group (K.Y., K.M.F., P.D.T., H.S.C., and K.A.D.), who used two methods to attempt to find the globally optimal conformations: "hydrophobic zippers" and a constraint-based hydrophobic core construction (CHCC) method. The CHCC method found global minima in all cases, and the hydrophobic zippers method found global minima in some cases, in minutes to hours on workstations. In 9 out of 10 sequences, the CHCC method found lower energy conformations than the 48-mers were designed to fold to. Thus the search strategies succeed for the HP model but the design strategy does not. For every sequence the global energy minimum was found to have multiple degeneracy with 10(3) to 10(6) conformations. We discuss the implications of these results for (i) searching conformational spaces of simple models of proteins and (ii) how these simple models relate to proteins.
DOI: 10.1073/pnas.92.1.325
PubMed: 7816842
Affiliations:
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Yue</name><affiliation><nlm:affiliation>Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-1204.</nlm:affiliation><wicri:noCountry code="subField">San Francisco 94143-1204</wicri:noCountry></affiliation></author><author><name sortKey="Fiebig, K M" sort="Fiebig, K M" uniqKey="Fiebig K" first="K M" last="Fiebig">K M Fiebig</name></author><author><name sortKey="Thomas, P D" sort="Thomas, P D" uniqKey="Thomas P" first="P D" last="Thomas">P D Thomas</name></author><author><name sortKey="Chan, H S" sort="Chan, H S" uniqKey="Chan H" first="H S" last="Chan">H S Chan</name></author><author><name sortKey="Shakhnovich, E I" sort="Shakhnovich, E I" uniqKey="Shakhnovich E" first="E I" last="Shakhnovich">E I Shakhnovich</name></author><author><name sortKey="Dill, K A" sort="Dill, K A" uniqKey="Dill K" first="K A" last="Dill">K A Dill</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="1995">1995</date><idno type="RBID">pubmed:7816842</idno><idno type="pmid">7816842</idno><idno type="doi">10.1073/pnas.92.1.325</idno><idno type="wicri:Area/PubMed/Corpus">002836</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002836</idno><idno type="wicri:Area/PubMed/Curation">002836</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002836</idno><idno type="wicri:Area/PubMed/Checkpoint">002700</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002700</idno><idno type="wicri:Area/Ncbi/Merge">002926</idno><idno type="wicri:Area/Ncbi/Curation">002926</idno><idno type="wicri:Area/Ncbi/Checkpoint">002926</idno><idno type="wicri:doubleKey">0027-8424:1995:Yue K:a:test:of</idno><idno type="wicri:Area/Main/Merge">004120</idno><idno type="wicri:Area/Main/Curation">004059</idno><idno type="wicri:Area/Main/Exploration">004059</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">A test of lattice protein folding algorithms.</title><author><name sortKey="Yue, K" sort="Yue, K" uniqKey="Yue K" first="K" last="Yue">K. Yue</name><affiliation><nlm:affiliation>Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-1204.</nlm:affiliation><wicri:noCountry code="subField">San Francisco 94143-1204</wicri:noCountry></affiliation></author><author><name sortKey="Fiebig, K M" sort="Fiebig, K M" uniqKey="Fiebig K" first="K M" last="Fiebig">K M Fiebig</name></author><author><name sortKey="Thomas, P D" sort="Thomas, P D" uniqKey="Thomas P" first="P D" last="Thomas">P D Thomas</name></author><author><name sortKey="Chan, H S" sort="Chan, H S" uniqKey="Chan H" first="H S" last="Chan">H S Chan</name></author><author><name sortKey="Shakhnovich, E I" sort="Shakhnovich, E I" uniqKey="Shakhnovich E" first="E I" last="Shakhnovich">E I Shakhnovich</name></author><author><name sortKey="Dill, K A" sort="Dill, K A" uniqKey="Dill K" first="K A" last="Dill">K A Dill</name></author></analytic><series><title level="j">Proceedings of the National Academy of Sciences of the United States of America</title><idno type="ISSN">0027-8424</idno><imprint><date when="1995" type="published">1995</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Amino Acid Sequence</term><term>Humans</term><term>Models, Molecular</term><term>Molecular Sequence Data</term><term>Protein Conformation</term><term>Protein Folding</term><term>Proteins (chemistry)</term><term>Reproducibility of Results</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Conformation des protéines</term><term>Données de séquences moléculaires</term><term>Humains</term><term>Modèles moléculaires</term><term>Pliage des protéines</term><term>Protéines ()</term><term>Reproductibilité des résultats</term><term>Séquence d'acides aminés</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Proteins</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Amino Acid Sequence</term><term>Humans</term><term>Models, Molecular</term><term>Molecular Sequence Data</term><term>Protein Conformation</term><term>Protein Folding</term><term>Reproducibility of Results</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Conformation des protéines</term><term>Données de séquences moléculaires</term><term>Humains</term><term>Modèles moléculaires</term><term>Pliage des protéines</term><term>Protéines</term><term>Reproductibilité des résultats</term><term>Séquence d'acides aminés</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We report a blind test of lattice-model-based search strategies for finding global minima of model protein chains. One of us (E.I.S.) selected 10 compact conformations of 48-mer chains on the three-dimensional cubic lattice and used their inverse folding algorithm to design HP (H, hydrophobic; P, polar) sequences that should fold to those "target" structures. The sequences, but not the structures, were sent to the UCSF group (K.Y., K.M.F., P.D.T., H.S.C., and K.A.D.), who used two methods to attempt to find the globally optimal conformations: "hydrophobic zippers" and a constraint-based hydrophobic core construction (CHCC) method. The CHCC method found global minima in all cases, and the hydrophobic zippers method found global minima in some cases, in minutes to hours on workstations. In 9 out of 10 sequences, the CHCC method found lower energy conformations than the 48-mers were designed to fold to. Thus the search strategies succeed for the HP model but the design strategy does not. For every sequence the global energy minimum was found to have multiple degeneracy with 10(3) to 10(6) conformations. We discuss the implications of these results for (i) searching conformational spaces of simple models of proteins and (ii) how these simple models relate to proteins.</div></front></TEI><affiliations><list></list><tree><noCountry><name sortKey="Chan, H S" sort="Chan, H S" uniqKey="Chan H" first="H S" last="Chan">H S Chan</name><name sortKey="Dill, K A" sort="Dill, K A" uniqKey="Dill K" first="K A" last="Dill">K A Dill</name><name sortKey="Fiebig, K M" sort="Fiebig, K M" uniqKey="Fiebig K" first="K M" last="Fiebig">K M Fiebig</name><name sortKey="Shakhnovich, E I" sort="Shakhnovich, E I" uniqKey="Shakhnovich E" first="E I" last="Shakhnovich">E I Shakhnovich</name><name sortKey="Thomas, P D" sort="Thomas, P D" uniqKey="Thomas P" first="P D" last="Thomas">P D Thomas</name><name sortKey="Yue, K" sort="Yue, K" uniqKey="Yue K" first="K" last="Yue">K. 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