Modeling study on the validity of a possibly simplified representation of proteins

Details Modeling study on the validity of a possibly simplified representation of proteins Modeling study on the validity of a possibly simplified representation of proteins

2000-06-23

arxiv.org/abs/physics/0006059v1

Phys. Rev. E Vol.61, No.6, 6981-6986 (June 2000)

Physics

Biological Physics

6 pages with 4 figures

Scientific paper

10.1103/PhysRevE.61.6981

The folding characteristics of sequences reduced with a possibly simplified representation of five types of residues are shown to be similar to their original ones with the natural set of residues (20 types or 20 letters). The reduced sequences have a good foldability and fold to the same native structure of their optimized original ones. A large ground state gap for the native structure shows the thermodynamic stability of the reduced sequences. The general validity of such a five-letter reduction is further studied via the correlation between the reduced sequences and the original ones. As a comparison, a reduction with two letters is found not to reproduce the native structure of the original sequences due to its homopolymeric features.

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