CONSTANT-TEMPERATURE SIMULATIONS OF HELIX FOLDING

This paper studies constant temperature (300 K) Monte Carlo simulation s of helix folding, carried out separately with short-range interactio ns only and with long-range interactions. The peptide -CONH-groups are treated as rigid elements to reduce the degrees of freedom. Non-dihed ral variables are used with flexible connections between the -CONH- an d C alpha to facilitate independent local motions. A 16-residue peptid e with alanine side chains is used as a model for helix folding. Start ing with an extended structure, the molecule folds into a-helical conf ormations. The simulations provide insight into the helix folding mech anism. Different potential functions are tested. With short-range inte ractions (10-12 potential) only, the helix folding is nearly random an d 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 sequen ce-dependent and the method does not indiscriminately force the backbo ne into the helix.