Molecular simulation of the reversible mechanical unfolding of proteins
In this work we have combined a Wang-Landau sampling scheme [F. Wang and D. Landau, Phys. Rev. Lett. 86, 2050 (2001)] with an expanded ensemble formalism to yield a simple and powerful method for computing potentials of mean force. The new method is implemented to investigate the mechanical deformat...
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| Veröffentlicht in: | The Journal of chemical physics 2004-03, Vol.120 (12), p.5781-5788 |
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| container_title | The Journal of chemical physics |
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| creator | Rathore, Nitin Yan, Qiliang de Pablo, Juan J |
| description | In this work we have combined a Wang-Landau sampling scheme [F. Wang and D. Landau, Phys. Rev. Lett. 86, 2050 (2001)] with an expanded ensemble formalism to yield a simple and powerful method for computing potentials of mean force. The new method is implemented to investigate the mechanical deformation of proteins. Comparisons are made with analytical results for simple model systems such as harmonic springs and Rouse chains. The method is then illustrated on a model 15-residue alanine molecule in an implicit solvent. Results for mechanical unfolding of this oligopeptide are compared to those of steered molecular dynamics calculations. |
| doi_str_mv | 10.1063/1.1649314 |
| format | Article |
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Wang and D. Landau, Phys. Rev. Lett. 86, 2050 (2001)] with an expanded ensemble formalism to yield a simple and powerful method for computing potentials of mean force. The new method is implemented to investigate the mechanical deformation of proteins. Comparisons are made with analytical results for simple model systems such as harmonic springs and Rouse chains. The method is then illustrated on a model 15-residue alanine molecule in an implicit solvent. 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| fulltext | fulltext |
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| ispartof | The Journal of chemical physics, 2004-03, Vol.120 (12), p.5781-5788 |
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| language | eng |
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| source | MEDLINE; AIP Journals Complete; AIP Digital Archive |
| subjects | Alanine - chemistry Computer Simulation Mathematics Oligopeptides - chemistry Protein Conformation Protein Folding Proteins - chemistry |
| title | Molecular simulation of the reversible mechanical unfolding of proteins |
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