Geometrically Reduced Number of Protein Ground State Candidates

Abstract

Geometrical properties of protein ground states are studied using an algebraic approach. It is shown that independent from inter-monomer interactions, the collection of ground state candidates for any folded protein is unexpectedly small: For the case of a two-parameter Hydrophobic-Polar lattice model for $L$-mers, the number of these candidates grows only as $L^2$. Moreover, the space of the interaction parameters of the model breaks up into well-defined domains, each corresponding to one ground state candidate, which are separated by sharp boundaries. In addition, by exact enumeration, we show there are some sequences which have one absolute unique native state. These absolute ground states have perfect stability against change of inter-monomer interaction potential.

9 page, 4 ps figures are included

References in corpus (1)

• Highly Designable Protein Structures and Inter Monomer Interactions

Cited by in corpus (7)

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• Statistical properties of contact vectors
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• Protein Ground State Candidates in a Simple Model: An Exact Enumeration
• One way to Characterize the compact structures of lattice protein model
• The Origin of the Designability of Protein Structures
• The Designability of Protein Structures: A Lattice-Model Study using the Miyazawa-Jernigan Matrix