Protein Ground State Candidates in a Simple Model: An Exact Enumeration

Abstract

The concept of the reduced set of contact maps is introduced. Using this concept we find the ground state candidates for Hydrophobic-Polar lattice model on a two dimensional square lattice. Using these results we exactly enumerate the native states of all proteins for a wide range of energy parameters. In this way, we show that there are some sequences, which have an absolute native state. Moreover, we study the scale-dependence of the number of the members of the reduced set, the number of ground state candidates, and the number of perfectly stable sequences by comparing the results for sequences with lengths of 6 up to 20.

7 pages in APS format + 17 figures (12 Postscript and 5 JPEG files)

References in corpus (4)

• Designability, thermodynamic stability, and dynamics in protein folding: a lattice model study
• Folding, Design and Determination of Interaction Potentials Using Off-Lattice Dynamics of Model Heteropolymers
• Statistical Properties of Contact Maps
• Geometrically Reduced Number of Protein Ground State Candidates

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