Journal of Physical Chemistry B, Vol.101, No.34, 6734-6740, 1997
Folding Pathways of a Helix-Turn-Helix Model Protein
A small model polypeptide represented in atomic detail is folded using Monte Carlo dynamics, The polypeptide is designed to have a native conformation similar to the central part of the helix-turn-helix protein ROP, Starting from a beta-strand conformation or two different loop conformations of the protein glutamine synthetase, six trajectories are generated using the so-called window move in dihedral angle space, This move changes conformations locally and leads to realistic, quasi-continuously evolving trajectories, Four of the six trajectories end in stable native-like conformations. Their folding pathways show a fast initial development of a helix-bend-helix motif, followed by a dynamic behavior predicted by the diffusion-collision model of Karplus and Weaver. The phenomenology of the pathways is consistent with experimental results.
Keywords:DIFFUSION-COLLISION MODEL;FLOW CIRCULAR-DICHROISM;STRUCTURAL CHARACTERIZATION;COMPUTER-SIMULATION;DYNAMICS SIMULATION;COMPLETE SEQUENCE;GLOBULAR PROTEIN;INTERMEDIATE;EQUILIBRIUM;INITIATION