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| Content Provider | World Health Organization (WHO)-Global Index Medicus |
|---|---|
| Author | Day, Ryan Daggett, Valerie |
| Description | Author Affiliation: Day R ( Biomolecular Structure and Design Program and Department of Medicinal Chemistry, University of Washington, Box 357610, Seattle, WA 98195-7610, USA.); |
| Abstract | Molecular dynamics (MD) simulations are the classic single-molecule 'experiments,' providing atomic-resolution structural and dynamic information. However, the single-molecule nature of the technique has also been its shortcoming, with frequent criticisms of sampling inadequacies and questions regarding the ensemble behavior of large numbers of molecules. Given the increase in computer power, we now address this issue by performing a large number of simulations and comparing individual and ensemble properties. One hundred independent MD simulations of the protein chymotrypsin inhibitor 2 were carried out for 20 ns each at 498 K in water to more fully describe the potentially diverse routes of protein unfolding and investigate how representative a single trajectory can be. Rapid unfolding was observed in all cases with the trajectories distributed about an average 'ensemble' path in which secondary and tertiary structure was lost concomitantly, with tertiary structure loss occurring slightly faster. Individual trajectories did, however, sample conformations far from the average path with very heterogeneous time-dependent properties. Nevertheless, all of the simulations but one followed the average ensemble pathway, such that a small number of simulations (5-10) are sufficient to capture the average properties of these states and the unfolding pathway. |
| ISSN | 00278424 |
| e-ISSN | 10916490 |
| Journal | Proceedings of the National Academy of Sciences of the United States of America |
| Issue Number | 38 |
| Volume Number | 102 |
| Language | English |
| Publisher | National Academy of Sciences |
| Publisher Date | 2005-09-01 |
| Publisher Place | United States |
| Access Restriction | Open |
| Subject Keyword | Models, Molecular Peptides Chemistry Protein Folding Hydrogen Bonding Nuclear Magnetic Resonance, Biomolecular Plant Proteins Protein Denaturation Protein Structure, Secondary Thermodynamics Research Support, N.I.H., Extramural Research Support, U.S. Gov't, P.H.S. Multidisciplinary |
| Content Type | Text |
| Resource Type | Article |
| Subject | Multidisciplinary |
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