Protein Folding as a Physical Stochastic Process

Details Protein Folding as a Physical Stochastic Process Protein Folding as a Physical Stochastic Process

2007-07-17

arxiv.org/abs/0707.2388v1

Physics

Condensed Matter

Soft Condensed Matter

20 pages, 15 figures, Keynote talk at BIOMAT2007, 24th-29th Nov, 2007, Brazil

Scientific paper

We model protein folding as a physical stochastic process as follows. The unfolded protein chain is treated as a random coil described by SAW (self-avoiding walk). Folding is induced by hydrophobic forces and other interactions, such as hydrogen bonding, which can be taken into account by imposing conditions on SAW. The resulting model is termed CSAW (conditioned self-avoiding walk. Conceptually, the mathematical basis is a generalized Langevin equation. In practice, the model is implemented on a computer by combining SAW and Monte Carlo. To illustrate the flexibility and capabilities of the model, we consider a number of examples, including folding pathways, elastic properties, helix formation, and collective modes.

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