A weighted HP model for protein folding with diagonal contacts
Böckenhauer, Hans-Joachim ; Bongartz, Dirk
RAIRO - Theoretical Informatics and Applications - Informatique Théorique et Applications, Tome 41 (2007), p. 375-402 / Harvested from Numdam

The HP model is one of the most popular discretized models for attacking the protein folding problem, i.e., for the computational prediction of the tertiary structure of a protein from its amino acid sequence. It is based on the assumption that interactions between hydrophobic amino acids are the main force in the folding process. Therefore, it distinguishes between polar and hydrophobic amino acids only and tries to embed the amino acid sequence into a two- or three-dimensional grid lattice such as to maximize the number of contacts, i.e., of pairs of hydrophobic amino acids that are embedded into neighboring positions of the grid. In this paper, we propose a new generalization of the HP model which overcomes one of the major drawbacks of the original HP model, namely the bipartiteness of the underlying grid structure which severely restricts the set of possible contacts. Moreover, we introduce the (biologically well-motivated) concept of weighted contacts, where each contact gets assigned a weight depending on the spatial distance between the embedded amino acids. We analyze the applicability of existing approximation algorithms for the original HP model to our new setting and design a new approximation algorithm for this generalized model.

Publié le : 2007-01-01
DOI : https://doi.org/10.1051/ita:2007023
Classification:  68W25,  92C40
@article{ITA_2007__41_4_375_0,
     author = {B\"ockenhauer, Hans-Joachim and Bongartz, Dirk},
     title = {A weighted HP model for protein folding with diagonal contacts},
     journal = {RAIRO - Theoretical Informatics and Applications - Informatique Th\'eorique et Applications},
     volume = {41},
     year = {2007},
     pages = {375-402},
     doi = {10.1051/ita:2007023},
     mrnumber = {2377969},
     zbl = {pre05301987},
     language = {en},
     url = {http://dml.mathdoc.fr/item/ITA_2007__41_4_375_0}
}
Böckenhauer, Hans-Joachim; Bongartz, Dirk. A weighted HP model for protein folding with diagonal contacts. RAIRO - Theoretical Informatics and Applications - Informatique Théorique et Applications, Tome 41 (2007) pp. 375-402. doi : 10.1051/ita:2007023. http://gdmltest.u-ga.fr/item/ITA_2007__41_4_375_0/

[1] R. Agarwala, S. Batzoglou, V. Dančík, S.E. Decatur, S. Hannenhalli, M. Farach, S. Muthukrishnan and S. Skiena, Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model. J. Comput. Biol. 4 (1997) 275-296.

[2] C.B. Anfinsen, Principles that govern the folding of protein chains. Science 181 (1973) 223-230.

[3] C.B. Anfinsen, E. Haber, M. Sela and F.H. White, The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. Proc. Natl. Acad. Sci. USA 47 (1961) 1309-1314.

[4] H.-J. Böckenhauer and D. Bongartz, Protein folding in the HP model on grid lattices with diagonals. Discrete Appl. Math. 155 (2007) 230-256. Extended Abstract in Proc. of the 29th International Symposium on Mathematical Foundations of Computer Science (MFCS'04). Lect. Notes Comput. Sci. 3153 (2004) 227-238. | Zbl 1097.92507

[5] V. Chandra, A. Dattasharma and V.S.A. Kumar, The algorithmics of folding proteins on lattices. Discrete Appl. Math. 127 (2003) 145-161. | Zbl 1038.92013

[6] P. Crescenzi, D. Goldman, C. Papadimitriou, A. Piccolboni and M. Yannakakis, On the complexity of protein folding. J. Comput. Biol. 5 (1998) 423-466. Extended Abstract in Proc. of the 30th Annual ACM Symposium on the Theory of Computing (STOC 1998) (1998) 597-603. | Zbl 1007.68511

[7] K.A. Dill, Theory for the folding and stability of globular proteins. Biochemistry 24 (1985) 1501.

[8] K.A. Dill, S. Bromberg, K. Yue, K. Fiebig, D. Yee, P. Thomas and H. Chan, Principles of protein folding - a perspective from simple exact models. Protein Sci. 4 (1995) 561-602.

[9] W.E. Hart and S. Istrail, Fast protein folding in the hydrophobic-hydrophilic model within three-eights of optimal. J. Comput. Biol. 3 (1996) 53-96.

[10] A. Newman, A New Algorithm for Protein Folding in the HP Model, in Proc. of the 13th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA'02) (2002) 876-884. | Zbl 1052.92026