Structural Determinant of Protein Designability

Details Structural Determinant of Protein Designability Structural Determinant of Protein Designability

2002-08-23

arxiv.org/abs/cond-mat/0208447v2

Physics

Condensed Matter

Soft Condensed Matter

4 pages, 3 figures, accepted to PRL 23.APR.03

Scientific paper

10.1103/PhysRevLett.90.218101

Here we present an approximate analytical theory for the relationship between a protein structure's contact matrix and the shape of its energy spectrum in amino acid sequence space. We demonstrate a dependence of the number of sequences of low energy in a structure on the eigenvalues of the structure's contact matrix, and then use a Monte Carlo simulation to test the applicability of this analytical result to cubic lattice proteins. We find that the lattice structures with the most low-energy sequences are the same as those predicted by the theory. We argue that, given sufficiently strict requirements for foldability, these structures are the most designable, and we propose a simple means to test whether the results in this paper hold true for real proteins.

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