A bias-exchange approach to protein folding
By suitably extending a recent approach [G. Bussi et al, J Am Chem Soc 2006, 128, 13435] we introduce a powerful methodology that allows the parallel reconstruction of the free energy of a system in a virtually unlimited number of variables. Multiple metadynamics simulations of the same system at th...
| Main Authors: | , |
|---|---|
| Format: | Journal Article |
| Published: |
American Chemical Society
2007
|
| Subjects: | |
| Online Access: | http://pubs.acs.org/cgi-bin/article.cgi/jpcbfk/2007/111/i17/pdf/jp067873l.pdf http://hdl.handle.net/20.500.11937/15651 |
| _version_ | 1848748951717543936 |
|---|---|
| author | Piana, Stefano Laio, A. |
| author_facet | Piana, Stefano Laio, A. |
| author_sort | Piana, Stefano |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | By suitably extending a recent approach [G. Bussi et al, J Am Chem Soc 2006, 128, 13435] we introduce a powerful methodology that allows the parallel reconstruction of the free energy of a system in a virtually unlimited number of variables. Multiple metadynamics simulations of the same system at the same temperature are performed, biasing each replica with a time-dependent potential constructed in a different set of collective variables. Exchanges between the bias potentials in the different variables are periodically allowed according to a replica exchange scheme. Due to the efficaciously multidimensional nature of the bias the method allows exploring complex free energy landscapes with high efficiency. The usefulness of the method is demonstrated by performing an atomistic simulation in explicit solvent of the folding of a Triptophane cage miniprotein. It is shown that the folding free energy landscape can be fully characterized starting from an extended conformation using only 40 ns of simulation on 8 replicas. |
| first_indexed | 2025-11-14T07:13:12Z |
| format | Journal Article |
| id | curtin-20.500.11937-15651 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-14T07:13:12Z |
| publishDate | 2007 |
| publisher | American Chemical Society |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-156512017-10-02T02:26:56Z A bias-exchange approach to protein folding Piana, Stefano Laio, A. Trp-cage protein folding molecular dynamics simulation free energy replica exchange Metadynamics By suitably extending a recent approach [G. Bussi et al, J Am Chem Soc 2006, 128, 13435] we introduce a powerful methodology that allows the parallel reconstruction of the free energy of a system in a virtually unlimited number of variables. Multiple metadynamics simulations of the same system at the same temperature are performed, biasing each replica with a time-dependent potential constructed in a different set of collective variables. Exchanges between the bias potentials in the different variables are periodically allowed according to a replica exchange scheme. Due to the efficaciously multidimensional nature of the bias the method allows exploring complex free energy landscapes with high efficiency. The usefulness of the method is demonstrated by performing an atomistic simulation in explicit solvent of the folding of a Triptophane cage miniprotein. It is shown that the folding free energy landscape can be fully characterized starting from an extended conformation using only 40 ns of simulation on 8 replicas. 2007 Journal Article http://hdl.handle.net/20.500.11937/15651 http://pubs.acs.org/cgi-bin/article.cgi/jpcbfk/2007/111/i17/pdf/jp067873l.pdf http://purl.org/au-research/grants/arc/DP0558938 American Chemical Society fulltext |
| spellingShingle | Trp-cage protein folding molecular dynamics simulation free energy replica exchange Metadynamics Piana, Stefano Laio, A. A bias-exchange approach to protein folding |
| title | A bias-exchange approach to protein folding |
| title_full | A bias-exchange approach to protein folding |
| title_fullStr | A bias-exchange approach to protein folding |
| title_full_unstemmed | A bias-exchange approach to protein folding |
| title_short | A bias-exchange approach to protein folding |
| title_sort | bias-exchange approach to protein folding |
| topic | Trp-cage protein folding molecular dynamics simulation free energy replica exchange Metadynamics |
| url | http://pubs.acs.org/cgi-bin/article.cgi/jpcbfk/2007/111/i17/pdf/jp067873l.pdf http://pubs.acs.org/cgi-bin/article.cgi/jpcbfk/2007/111/i17/pdf/jp067873l.pdf http://hdl.handle.net/20.500.11937/15651 |