Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model

Richa Agarwala, Serafim Batzoglou, Vlado Dancik, Scott E. Decatur, Martin Farach, Sridhar Hannenhalli, Steven Skiena

Research output: Contribution to conferencePaperpeer-review

12 Scopus citations

Abstract

We consider the problem of determining the three-dimensional folding of a protein given its one-dimensional amino acid sequence. We use the HP model for protein folding proposed by Dill, which models protein as a chain of amino acid residues that are either hydrophobic or polar, and hydrophobic interactions are the dominant initial driving force for the protein folding. Hart and Istrail gave approximation algorithms for folding proteins on the cubic lattice under HP model. In this paper, we examine the choice of a lattice by considering its algorithmic and geometric implications and argue that triangular lattice is a more reasonable choice. We present a set of folding rules for a triangular lattice and analyze the approximation ratio which they achieve. In addition, we introduce a generalization of the HP model to account for residues having different levels of hydrophobicity. After describing the biological foundation for this generalization, we show that in the new model we are able to achieve similar constant factor approximation guarantees on the triangular lattice as were achieved in the standard HP model. While the structures derived from our folding rules are probably still far from biological reality, we hope that having a set of folding rules with different properties will yield more interesting folds when combined.

Original languageEnglish (US)
Pages390-399
Number of pages10
StatePublished - 1997
Externally publishedYes
EventProceedings of the 1996 8th Annual ACM-SIAM Symposium on Discrete Algorithms - New Orleans, LA, USA
Duration: Jan 5 1997Jan 7 1997

Other

OtherProceedings of the 1996 8th Annual ACM-SIAM Symposium on Discrete Algorithms
CityNew Orleans, LA, USA
Period1/5/971/7/97

All Science Journal Classification (ASJC) codes

  • Software
  • Mathematics(all)

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