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Journal of Biological Physics

, Volume 28, Issue 1, pp 1–15 | Cite as

Enumerating Designing Sequences in the HP Model

  • Anders Irbäck
  • Carl Troein
Article

Abstract

The hydrophobic/polar HP model on the square lattice has been widely used toinvestigate basics of protein folding. In the cases where all designing sequences (sequences with unique ground states) were enumerated without restrictions on the number of contacts, the upper limit on the chain length N has been 18–20 because of the rapid exponential growth of thenumbers of conformations and sequences. We show how a few optimizations push this limit by about 5 units. Based on these calculations, we study the statistical distribution of hydrophobicity along designing sequences. We find that the average number of hydrophobic and polar clumps along the chains is larger for designing sequences than for random ones, which is in agreement with earlier findings for N ≤ 18 and with results for real enzymes. We also show that this deviation from randomness disappears if the calculations are restricted to maximally compact structures.

exact enumeration folding thermodynamics hydrophobicity correlations hydrophobic/polar lattice model protein folding protein sequence analysis 
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© Kluwer Academic Publishers 2002

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  • Anders Irbäck
  • Carl Troein

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