Name
Title | ||
|---|---|---|
Matching simulation and experiment (extended abstract): a new simplified model for simulating protein folding |
Abstract | ||
|---|---|---|
Simulations of simplified protein folding models have provided much insight into solving the protein folding problem. We propose here a new off-lattice bead model, capable of simulating several different fold classes of small proteins. We present the sequence for an &agr;/&bgr; protein resembling the IgG-binding proteins L and G. The thermodynamics of the folding process for this model are characterized using the multiple multi-histogram method combined with constant-temperature Langevin simulations. The folding is shown to be highly cooperative, with chain collapse nearly accompanying folding. Two parallel folding pathways are shown to exist on the folding free energy landscape. One pathway contains an intermediate—similar to experiments on protein G, and one pathway contains no intermediates—similar to experiments on protein L. The folding kinetics are characterized by tabulating mean-first passage times, and we show that the onset of glasslike kinetics occurs at much lower temperatures than the folding temperature. This model is expected to be useful in many future contexts; investigating questions of the role of local versus non-local interactions in various fold classes, addressing the effect of sequence mutations affecting secondary structure propensities, and providing a computationally feasible model for studying the role of solvation forces in protein folding. |
Year | DOI | Venue |
|---|---|---|
2000 | 10.1145/332306.332565 | RECOMB |
Keywords | Field | DocType |
simulating protein folding,protein folding problem,matching simulation,accompanying folding,protein folding,protein g,folding free energy landscape,folding process,folding kinetics,folding temperature,parallel folding pathway,protein folding model,structural genomics,clustering | Protein folding,Structural genomics,Biology,Protein G,Solvation,Bioinformatics,Statistical Mode,Kinetics,Protein secondary structure,Energy landscape | Conference |
ISBN | Citations | PageRank |
1-58113-186-0 | 0 | 0.34 |
References | Authors | |
1 | 2 | |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Jon M. Sorenson | 1 | 2 | 1.13 |
| Teresa Head-Gordon | 2 | 27 | 6.25 |