Abstract
Lattice protein models are used for hierarchical approaches to protein structure prediction, as well as for investigating principles of protein folding. So far, one has the problem that there exists no lattice that can model real protein conformations with good quality and for which an efficient method to find native conformations is known.
We present the first method for the FCC-HP-Model [3] that is capable of finding native conformations for real-sized HP-sequences. It has been shown [23] that the FCC lattice can model real protein conformations with coordinate root mean square deviation below 2 Å.
Our method uses a constraint-based approach. It works by first calculating maximally compact sets of points (hydrophobic cores), and then threading the given HP-sequence to the hydrophobic cores such that the core is occupied by H-monomers.
Supported by the PhD programme “Graduiertenkolleg Logik in der Informatik” (GKLI) of the “Deutsche Forschungsgemeinschaft” (DFG).
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
V. I. Abkevich, A. M. Gutin, and E. I. Shakhnovich. Impact of local and nonlocal interactions on thermodynamics and kinetics of protein folding. Journal of Molecular Biology, 252:460–471, 1995.
V.I. Abkevich, A.M. Gutin, and E.I. Shakhnovich. Computer simulations of prebiotic evolution. In Russ B. Altman, A. Keith Dunker, Lawrence Hunter, and Teri E. Klein, editors, PSB’97, pages 27–38, 1997.
Richa Agarwala, Serafim Batzoglou, Vlado Dancik, Scott E. Decatur, Martin Farach, Sridhar Hannenhalli, S. Muthukrishnan, and Steven Skiena. Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP-model. Journal of Computational Biology, 4(2):275–296, 1997.
Rolf Backofen. Constraint techniques for solving the protein structure prediction problem. In Michael Maher and Jean-Francois Puget, editors, Proceedings of 4 thInternational Conference on Principle and Practice of Constraint Programming (CP’98), volume 1520 of Lecture Notes in Computer Science, pages 72–86. Springer Verlag, 1998.
Rolf Backofen. An upper bound for number of contacts in the HP-model on the face-centered-cubic lattice (FCC). In Raffaele Giancarlo and David Sanko., editors, Proc. of the 11th Annual Symposium on Combinatorial Pattern Matching (CPM2000), volume 1848 of Lecture Notes in Computer Science, pages 277–292, Berlin, 2000. Springer-Verlag.
Rolf Backofen and Sebastian Will. Optimally compact finite sphere packings — hydrophobic cores in the FCC. In Amihood Amir and Gad Landau, editors, Proc. of the 12th Annual Symposium on Combinatorial Pattern Matching (CPM2001), volume 2089 of Lecture Notes in Computer Science, pages 257–271, Berlin, 2001. Springer-Verlag.
Rolf Backofen, Sebastian Will, and Erich Bornberg-Bauer.Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets. J. Bioinformatics, 15(3):234–242, 1999.
Rolf Backofen, Sebastian Will, and Peter Clote. Algorithmic approach to quantifying the hydrophobic force contribution in protein folding. In Russ B. Altman, A. Keith Dunker, Lawrence Hunter, and Teri E. Klein, editors, Pacific Symposium on Biocomputing (PSB 2000), volume 5, pages 92–103, 2000.
U Bastolla, H Frauenkron, E Gerstner, P Grassberger, and W Nadler. Testing a new monte carlo algorithm for protein folding. Proteins, 32(1):52–66, 1998.
B. Berger and T. Leighton. Protein folding in the hydrophobic-hydrophilic (HP) modell is NP-complete. In Proc. of the Second Annual International Conferences on Compututational Molecular Biology (RECOMB98), pages 30–39, New York, 1998.
Erich Bornberg-Bauer. Chain growth algorithms for HP-type lattice proteins. In Proc. of the 1 stAnnual International Conference on Computational Molecular Biology (RECOMB), pages 47–55. ACM Press, 1997.
P. Crescenzi, D. Goldman, C. Papadimitriou, A. Piccolboni, and M. Yannakakis. On the complexity of protein folding. In Proc. of STOC, pages 597–603, 1998. Short version in Proc. of RECOMB’98, pages 61-62.
K.A. Dill, S. Bromberg, K. Yue, K.M. Fiebig, D.P. Yee, P.D. Thomas, and H.S. Chan. Principles of protein folding-a perspective of simple exact models. Protein Science, 4:561–602, 1995.
Ken A. Dill, Klaus M. Fiebig, and Hue Sun Chan. Cooperativity in protein-folding kinetics. Proc. Natl. Acad. Sci. USA, 90:1942–1946, 1993.
Aaron R. Dinner, Andreaj Šali, and Martin Karplus. The folding mechanism of larger model proteins: Role of native structure. Proc. Natl. Acad. Sci. USA, 93:8356–8361, 1996.
Eugene C. Freuder. A sufficient condition for backtrack-free search. Journal of the Association for Computing Machinery, 29(1):24–32, 1982.
S. Govindarajan and R. A. Goldstein. The foldability landscape of model proteins. Biopolymers, 42(4):427–438, 1997.
Patrice Koehl and Michael Levitt. A brighter future for protein structure prediction. Nature Structural Biology, 6:108–111, 1999.
Kit Fun Lau and Ken A. Dill. A lattice statistical mechanics model of the conformational and sequence spaces of proteins. Macromolecules, 22:3986–3997, 1989.
Hao Li, Robert Helling, Chao Tnag, and Ned Wingreen. Emergence of preferred structures in a simple model of protein folding. Science, 273:666–669, 1996.
Neil Madras and Gordon Slade. The Self-Avoiding Walk. Probability and Its Applications. Springer, 1996.
Tobias Müller and Jörg Würtz. Interfacing propagators with a concurrent constraint language. In JICSLP96 Post-conference workshop and Compulog Net Meeting on Parallelism and Implementation Technology for (Constraint) Logic Programming Languages, pages 195–206, 1996.
Britt H. Park and Michael Levitt. The complexity and accuracy of discrete state models of protein structure. Journal of Molecular Biology, 249:493–507, 1995.
J.-C. Regin. A filtering algorithm for constraints of difference in CSPs. In Proc. 12th Conf. American Assoc. Artificial Intelligence, volume 1, pages 362–367. Amer. Assoc. Artificial Intelligence, 1994.
Gert Smolka. The Oz programming model. In Jan van Leeuwen, editor, Computer Science Today, Lecture Notes in Computer Science, vol. 1000, pages 324–343. Springer-Verlag, Berlin, 1995.
R. Unger and J. Moult. Genetic algorithms for protein folding simulations. Journal of Molecular Biology, 231:75–81, 1993.
Ron Unger and John Moult. Local interactions dominate folding in a simple protein model. Journal of Molecular Biology, 259:988–994, 1996.
A. Šali, E. Shakhnovich, and M. Karplus. Kinetics of protein folding. Journal of Molecular Biology, 235:1614–1636, 1994.
Yu Xia, Enoch S. Huang, Michael Levitt, and Ram Samudrala. Ab initio construction of protein tertiary structures using a hierarchical approach. Journal of Molecular Biology, 300:171–185, 2000.
Kaizhi Yue and Ken A. Dill. Forces of tertiary structural organization in globular proteins. Proc. Natl. Acad. Sci. USA, 92:146–150, 1995.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2001 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Backofen, R., Will, S. (2001). Fast, Constraint-Based Threading of HP-Sequences to Hydrophobic Cores. In: Walsh, T. (eds) Principles and Practice of Constraint Programming — CP 2001. CP 2001. Lecture Notes in Computer Science, vol 2239. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45578-7_34
Download citation
DOI: https://doi.org/10.1007/3-540-45578-7_34
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-42863-3
Online ISBN: 978-3-540-45578-3
eBook Packages: Springer Book Archive