Folding very short peptides using molecular dynamics.
Peptides often have conformational preferences. We simulated 133 peptide 8-mer fragments from six different proteins, sampled by replica-exchange molecular dynamics using Amber7 with a GB/SA (generalized-Born/solvent-accessible electrostatic approximation to water) implicit solvent. We found that 85...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2006-04-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.0020027 |
| _version_ | 1818722882142863360 |
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| author | Bosco K Ho Ken A Dill |
| author_facet | Bosco K Ho Ken A Dill |
| author_sort | Bosco K Ho |
| collection | DOAJ |
| description | Peptides often have conformational preferences. We simulated 133 peptide 8-mer fragments from six different proteins, sampled by replica-exchange molecular dynamics using Amber7 with a GB/SA (generalized-Born/solvent-accessible electrostatic approximation to water) implicit solvent. We found that 85 of the peptides have no preferred structure, while 48 of them converge to a preferred structure. In 85% of the converged cases (41 peptides), the structures found by the simulations bear some resemblance to their native structures, based on a coarse-grained backbone description. In particular, all seven of the beta hairpins in the native structures contain a fragment in the turn that is highly structured. In the eight cases where the bioinformatics-based I-sites library picks out native-like structures, the present simulations are largely in agreement. Such physics-based modeling may be useful for identifying early nuclei in folding kinetics and for assisting in protein-structure prediction methods that utilize the assembly of peptide fragments. |
| first_indexed | 2024-12-17T21:01:41Z |
| format | Article |
| id | doaj.art-9ccfa3ae784740949c541e4a4e37d9d8 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-17T21:01:41Z |
| publishDate | 2006-04-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-9ccfa3ae784740949c541e4a4e37d9d82022-12-21T21:32:42ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582006-04-0124e2710.1371/journal.pcbi.0020027Folding very short peptides using molecular dynamics.Bosco K HoKen A DillPeptides often have conformational preferences. We simulated 133 peptide 8-mer fragments from six different proteins, sampled by replica-exchange molecular dynamics using Amber7 with a GB/SA (generalized-Born/solvent-accessible electrostatic approximation to water) implicit solvent. We found that 85 of the peptides have no preferred structure, while 48 of them converge to a preferred structure. In 85% of the converged cases (41 peptides), the structures found by the simulations bear some resemblance to their native structures, based on a coarse-grained backbone description. In particular, all seven of the beta hairpins in the native structures contain a fragment in the turn that is highly structured. In the eight cases where the bioinformatics-based I-sites library picks out native-like structures, the present simulations are largely in agreement. Such physics-based modeling may be useful for identifying early nuclei in folding kinetics and for assisting in protein-structure prediction methods that utilize the assembly of peptide fragments.https://doi.org/10.1371/journal.pcbi.0020027 |
| spellingShingle | Bosco K Ho Ken A Dill Folding very short peptides using molecular dynamics. PLoS Computational Biology |
| title | Folding very short peptides using molecular dynamics. |
| title_full | Folding very short peptides using molecular dynamics. |
| title_fullStr | Folding very short peptides using molecular dynamics. |
| title_full_unstemmed | Folding very short peptides using molecular dynamics. |
| title_short | Folding very short peptides using molecular dynamics. |
| title_sort | folding very short peptides using molecular dynamics |
| url | https://doi.org/10.1371/journal.pcbi.0020027 |
| work_keys_str_mv | AT boscokho foldingveryshortpeptidesusingmoleculardynamics AT kenadill foldingveryshortpeptidesusingmoleculardynamics |