title: Proteins with selected sequences: a heteropolymeric study.
abstract: Protein sequences are expected not to be random but selected in order to form a stable native structure that is kinetically accessible. Therefore our model contains a selective temperature in sequence space (see [S. Ramanathan and E. Shakhnovich, Phys. Rev. E 50, 1303 (1994)] ) to optimize the sequence for the target conformation statistically. Replica calculations, which go beyond quadratic approximations in the field-theoretical Hamiltonian, are presented. A phase diagram indicating the temperatures and selective temperatures at which transitions to a frozen globule, i.e., the native state, occur is obtained. It is shown that going beyond the quadratic approximation in the field Hamiltonian is very important, since it results in a significant change of the phase diagram. Moreover, we suggest that a one-step replica permutation symmetry scheme is sufficient to solve the model. In addition to this we present a result for the sequence correlation function along the chain in the case of a short-ranged potential between the monomers. A correlation function between monomers that form a contact in the native state is given depending on the temperature and the interaction parameter.
authors: Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA. juergen@chasma.harvard.edu
authors: J
authors: J
authors: Wilder
authors: E I
authors: EI
authors: Shakhnovich
mesh_terms: D000595:Amino Acid Sequence; D019277:Entropy; D008962:Models, Theoretical; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013696:Temperature
chemical_list: D011506:Proteins