Using the HP model find the energies for the following confo

Using the HP model, find the energies for the following conformations of the 13-site sequence: HHHHHHHPHHPHP:

Solution

The HP Model ( Hydrophobic/Polar) is a simple one-parameter model that provides a way of understanding the ground states of the folded polymers and how they unfold with increasing temperature. In the model, every amino acid is classified as either hydrophobic (H) or polar (P): the H group has 9 amino acids ( alanine, cysteine, isoleucine, leucine, methionine, phenylalanine, tryptophan, tyrosine, valine) while the P has 11 (Arginine, aspargine, aspartic acid, glutamic acid,glutamine, glycine, histadine, lysine, proline, serine, threonine).

Here all interactions between one amino acid and another or its aqueous environment are zero with the exception that hydrophobic species have a repulsive energy +_H with any polar species or the environment: nearest neighbor covalent bonds are not part of this accounting.

In the example shown, the straight line is a completely unfolded configuration while the two other states are compact. One of these compact states is metastable, with 5 HH contacts (repulsive energy= +11_H ) while the other is the true ground state with 6 HH contacts ( energy= +9_H ). The metastable configuration can only reach the ground state through a series of moves that take it through states with significantly higher energy.

Thus (b) would be \'metastable\' = +11_H and (c) would be \'ground state\' = +9_H