Lattice protein

Lattice proteins are highly simplified computer models of proteins which are used to investigate protein folding.

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Because proteins are such large molecules, containing hundreds or thousands of atoms, it is not possible with current technology to simulate more than a few microseconds of their behaviour in all-atom detail. Hence real proteins cannot be folded on a computer. Lattice proteins, however, are simplified in two ways: the amino acids are modelled as single "beads" rather than modeling every atom, and the beads are restricted to a rigid (usually cubic) lattice. This simplification means they can fold to their energy minima in a time quick enough to be simulated.

Lattice proteins are made to resemble real proteins by introducing an energy function, a set of conditions which specify the energy of interaction between neighbouring beads, usually taken to be those occupying adjacent lattice sites. The energy function mimics the interactions between amino acids in real proteins, which include steric, hydrophobic and hydrogen bonding effects. The beads are divided into types, and the energy function specifies the interactions depending on the bead type, just as different types of amino acids interact differently. One of the most popular lattice models, the HP model, features just two bead types - hydrophobic (H) and polar (P) - and mimics the hydrophobic effect by specifying a negative (favourable) interaction between H beads.

For any sequence in any particular structure, an energy can be rapidly calculated from the energy function. For the simple HP model, this is simply an enumeration of all the contacts between H residues that are adjacent in the structure, but not in the chain. Most researchers consider a lattice protein sequence protein-like only if it possesses a single structure with an energetic state lower than in any other structure. This is the energetic ground state, or native state. The relative positions of the beads in the native state constitute the lattice protein's tertiary structure. Lattice proteins do not have genuine secondary structure, although some researchers have claimed that they can be extrapolated to real protein structures which do include secondary structure, by appealing to the same law by which the phase diagrams of different substances can be scaled onto one another.

By varying the energy function and the bead sequence of the chain (the primary structure), effects on the native state structure and the kinetics (rate) of folding can be explored, and this may provide insights into the folding of real proteins. In particular, lattice models have been used to investigate the energy landscapes of proteins, i.e. the variation of their internal free energy as a function of conformation.

References

• Kit Fun Lau, Ken A. Dill. A lattice statistical mechanics model of the conformational and sequence spaces of proteins. Macromolecules 1989, 22, 3986-3997.