page_title: Lattice protein
section_title: Hydrophobic-polar model
hierarchical_section_title: Lattice protein / Hydrophobic-polar model
caption_attribution_description: English: A thermodynamically unstable conformation of a generic polypeptide. Hydrophobic residues are in green while polar residues are in blue.
context_page_description: Lattice proteins are highly simplified models of protein-like heteropolymer chains on lattice conformational space which are used to investigate protein folding. Simplification in lattice proteins is twofold: each whole residue is modeled as a single "bead" or "point" of a finite set of types, and each residue is restricted to be placed on vertices of a lattice. To guarantee the connectivity of the protein chain, adjacent residues on the backbone must be placed on adjacent vertices of the lattice. Steric constraints are expressed by imposing that no more than one residue can be placed on the same lattice vertex.
  Because proteins are such large molecules, there are severe computational limits on the simulated timescales of their behaviour when modeled in all-atom detail. The millisecond regime for all-atom simulations was not reached until 2010, and it is still not possible to fold all real proteins on a computer. Simplification significantly reduces the computational effort in handling the model, although even in this simplified scenario the protein folding problem is NP-complete.
context_section_description: The hydrophobic-polar protein model is the original lattice protein model. It was first proposed by Dill et. al. in 1985 as a way to overcome the significant cost and difficulty of predicting protein structure, using only the hydrophobicity of the amino acids in the protein to predict the protein structure. It is considered to be the paradigmatic lattice protein model. The method was able to quickly give an estimate of protein structure by representing proteins as "short chains on a 2D square lattice" and has since become known as the hydrophobic-polar model. It breaks the protein folding problem into three separate problems: modeling the protein conformation, defining the energetic properties of the amino acids as they interact with one another to find said conformation, and developing an efficient algorithm for the prediction of these conformations. It is done by classifying amino acids in the protein as either hydrophobic or polar and assuming that the protein is being folded in an aqueous environment. The lattice statistical model seeks to recreate protein folding by minimizing the free energy of the contacts between hydrophobic amino acids. Hydrophobic amino acid residues are predicted to group around each other, while hydrophilic residues interact with the surrounding water.
  Different lattice types and algorithms were used to study protein folding with HP model. Efforts were made to obtain higher approximation ratios using approximation algorithms in 2 dimensional and 3 dimensional, square and triangular lattices. Alternative to approximation algorithms, some genetic algorithms were also exploited with square, triangular, and face-centered-cubic lattices.
caption: A schematic of a thermodynamically unstable conformation of a generic polypeptide. Note the lower number of hydrophobic contacts than above. Hydrophobic residues are in green and polar residues are in blue.
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