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

摘要

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 (epsilon(hel) = 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. (C) 2004 Elsevier Ltd. All rights reserved.