The effect of sequence patterns and local conformational preferences on the structure of collapsed polypeptide

We studied the structure of a polypeptide model by means of the Monte Carlo method. The model chain consisting of two kinds of residues (hydrophobic a nd hydrophilic) was confined on the (310) hybrid lattice. The residues inte racted with the long-range contact potential. The short-range potential was also used by introducing the preferences of conformations corresponding to the helical structure. Simulations of the coil-to-globule collapse were do ne by an annealing process starting from high-temperature structures and th en gradual cooling of the system. The parameters describing the behavior of the system were monitored. It has been found that in a case of a helical p attern -HHPPHPP- the collapsed chains consisted of helical fragments. The r esulting structures were formed in such way that the polar residues were lo cated in the outer shell of the molecular since the hydrophobic residues fi lled the inner part of molecule. The results showed that the proper balance between the magnitude of the potentials used in a model is important and i ts influence on final structures of molecules was discussed. (C) 2000 John Wiley & Sons, Inc.