Structural Determinant of Protein Designability

Jeremy L. England; Eugene I. Shakhnovich

doi:10.1103/physrevlett.90.218101

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arXiv · cond-mat/0208447

Structural Determinant of Protein Designability

Jeremy L. England·Eugene I. Shakhnovich

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Abstract

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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Jeremy L. England, Eugene I. Shakhnovich. 2003-04-22. Structural Determinant of Protein Designability. https://doi.org/10.1103/physrevlett.90.218101

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