- Lattice protein
Lattice proteins are highly simplified computer models of
protein s which are used to investigateprotein folding .Because proteins are such large
molecule s, containing hundreds or thousands ofatom s, it is not possible with current technology to simulate more than a fewmicrosecond s of their behaviour in all-atom detail. Hence real proteins cannot be folded on a computer. Lattice proteins, however, are simplified in two ways: theamino acid s 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 andhydrogen 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, theHP model , features just two bead types -hydrophobic (H) and polar (P) - and mimics thehydrophobic 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'stertiary structure . Lattice proteins do not have genuinesecondary 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 thephase diagram s 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 theenergy landscape s 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.
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