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Backbone dynamics, fast folding, and secondary structure formation in helical proteins and peptides

✍ Scribed by Corey Hardin; Zaida Luthey-Schulten; Peter G. Wolynes

Publisher
John Wiley and Sons
Year
1999
Tongue
English
Weight
214 KB
Volume
34
Category
Article
ISSN
0887-3585

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✦ Synopsis

We discuss the construction of a simple, off-lattice model protein with a comparatively detailed representation of the protein backbone, and use it to address some general aspects of the folding kinetics of a small helical protein and two peptide fragments. The model makes use of an associative memory hamiltonian to smoothly interpolate between the limits of a native contact only, or Go, potential and a statistical pair potential derived from a database of known structures. We have observed qualitatively different behavior in these two limits. In the Go limit, we see apparently barrier-less folding. As we increase the roughness of the model energy landscape, we can observe the emergence of the characteristic activated temperature dependence previously seen in lattice studies and analytical theories. We are also able to study the dependence of the folding kinetics on local interactions such as hydrogen bonds, and we discuss the implications of these results for the formation of secondary structure at intermediate stages of the folding reaction.

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