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...
Guardado en:
| Autores principales: | , |
|---|---|
| Formato: | article |
| Lenguaje: | EN |
| Publicado: |
Public Library of Science (PLoS)
2006
|
| Materias: | |
| Acceso en línea: | https://doaj.org/article/9ccfa3ae784740949c541e4a4e37d9d8 |
| Etiquetas: |
Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
|
| id |
oai:doaj.org-article:9ccfa3ae784740949c541e4a4e37d9d8 |
|---|---|
| record_format |
dspace |
| spelling |
oai:doaj.org-article:9ccfa3ae784740949c541e4a4e37d9d82021-11-25T05:41:07ZFolding very short peptides using molecular dynamics.1553-734X1553-735810.1371/journal.pcbi.0020027https://doaj.org/article/9ccfa3ae784740949c541e4a4e37d9d82006-04-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.0020027https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Peptides 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.Bosco K HoKen A DillPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 2, Iss 4, p e27 (2006) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Biology (General) QH301-705.5 |
| spellingShingle |
Biology (General) QH301-705.5 Bosco K Ho Ken A Dill Folding very short peptides using molecular dynamics. |
| 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. |
| format |
article |
| author |
Bosco K Ho Ken A Dill |
| author_facet |
Bosco K Ho Ken A Dill |
| author_sort |
Bosco K Ho |
| title |
Folding very short peptides using molecular dynamics. |
| title_short |
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_sort |
folding very short peptides using molecular dynamics. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2006 |
| url |
https://doaj.org/article/9ccfa3ae784740949c541e4a4e37d9d8 |
| work_keys_str_mv |
AT boscokho foldingveryshortpeptidesusingmoleculardynamics AT kenadill foldingveryshortpeptidesusingmoleculardynamics |
| _version_ |
1718414533905612800 |