Effect of secondary structure on the conformations and folding behaviors of protein-like chains

We present a new model considering the effects of secondary structure on the conformations and folding process of protein-like chains in three-dimensional simple cubic lattice in this paper. The properties such as chain dimensions, shape, average contacts and chain average energy with different helical energy of a helix (εhel=0, −0.75, −1.5, and −3 in the unit of kT) are discussed here. Unlike conventional polymers, protein-like chains are much compact. We also find that the ability to form helix of residue is different under the condition of different helical energy of a helix. The energy distribution for protein-like chains with different length and the conformation changes in the process of folding of proteins are discussed. Comparisons with real protein chains are also made.