Computer simulation of the folding of coiled coils

©1994 American Institute of PhysicsThe electronic version of this article is the complete one and can be found online at: http://link.aip.org/link/?JCPSA6/100/2267/1DOI:10.1063/1.466525A simple model capable of providing possible folding pathways of two stranded, coiled coil peptides is described and simulated using an off-lattice dynamic Monte Carlo algorithm. Short sequences of very regular repetitive blocks of amino acids are studied. The regularity of the sequence is enhanced by a simplified interaction scale between pairs of residues. Following the transition from two isolated chains in a random conformation to the folded dimeric structure, the main features capable of obtaining a parallel, in-register, unique conformation, are examined. These include the geometrical representation of the model, the cooperative development of secondary and tertiary structures, and the role of tertiary interactions stabilizing the coiled coil geometry. The influence of introducing disulfide bridges in certain locations of the sequence is also discussed