Hydrophobic-polar protein folding model

Hydrophobic-polar protein folding model

The hydrophobic-polar protein folding model is a highly simplified model for examining protein folds in space. First proposed by Dill in 1985, it is motivated by the observation that hydrophobic interactions between amino acid residues are the driving force for proteins folding into their native state.cite journal |author=Dill K.A. |title=Theory for the folding and stability of globular proteins |journal=Biochemistry |volume=24 |issue=1501 |year=1985 |id=Entrez Pubmed|3986190 |doi=10.1021/bi00327a032 |pages=1501] All amino acid types are classified as either hydrophobic (H) or polar (P), and the folding of a protein sequence is defined as a self-avoiding walk in a 2D or 3D lattice. The HP model imitates the hydrophobic effect by assigning a negative (favorable) weight to interactions between adjacent, non-covalently bound H residues. Proteins that have minimum energy are assumed to be in their native state.

The HP model can be expressed in both two and three dimensions, generally with square lattices, although triangular lattices have been used as well.

Randomized search algorithms are often used to tackle the HP folding problem. This includes stochastic, evolutionary algorithms like the Monte Carlo method, genetic algorithms, and ant colony optimization. While no method has been able to calculate the experimentally determined minimum energetic state for long protein sequences, the most advanced methods today are able to come close.cite journal |author=Bui T.N., Sundarraj G. |title=An efficient genetic algorithm for predicting protein tertiary structures in the 2D HP model |journal=GECCO'05 |year=2005 |doi=10.1145/1068009.1068072 |pages=385 ] cite journal |author=Shmygelska A., Hoos H.H. |title=An improved ant colony optimisation algorithm for the 2D HP protein folding problem |journal=Proc. of the 16th Canadian Conference on Artificial Intelligence (AI'2003)|volume=2671 |pages=400–417 |year=2003]

Even though the HP model abstracts away many of the details of protein folding, it is still an NP-hard problem on both 2D and 3D lattices.cite journal |author=Crescenzi P., Goldman D., Papadimitriou C., Piccolboni A., Yannakakis M. |title=On the complexity of protein folding |journal=Macromolecules |volume=5 |issue=1 |pages=27–40 |year=1998 |id=Entrez Pubmed|9773342]

Recently, a Monte Carlo method, named FRESS, was developed and appears to perform well on HP models. cite journal |author=Jinfeng Zhang, S. C. Kou, Jun S. Liu | title=Polymer structure optimization and simulation via a fragment re-growth Monte Carlo |journal=J. Chem. Phys. |volume=126 |pages=225101 |year=2007|id=Entrez Pubmed|17581081 | doi=10.1063/1.2736681]

ee also

* Protein structure prediction
* Lattice proteins

References


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