Constant temperature simulations of helix folding

Abstract

This paper studies constant temperature (300 K) Monte Carlo simulations of helix folding, carried out separately with short-range interactions only and with long-range interactions. The peptide -CONH-groups are treated as rigid elements to reduce the degrees of freedom. Non-dihedral variables are used with flexible connections between the -CONH- and Cα to facilitate independent local motions. A 16-residue peptide with alanine side chains is used as a model for helix folding. Starting with an extended structure, the molecule folds into α-helical conformations. The simulations provide insight into the helix folding mechanism. Different potential functions are tested. With short-range interactions (10-12 potential) only, the helix folding is nearly random and is much slower than that with long-range electrostatic interactions. This observation indicates that the spatially long-range interaction is essential for rapid folding of the helix. Under the same conditions, polyglycine does not fold into stable helices. The folding is sequence-dependent and the method does not indiscriminately force the backbone into the helix.