Folding pathways of a helix-turn-helix model protein

Details Folding pathways of a helix-turn-helix model protein Folding pathways of a helix-turn-helix model protein

1997-06-11

arxiv.org/abs/physics/9706018v1

Physics

Biological Physics

24 pages, LaTeX, 6 figures, to appear in J. Phys. Chem., see also chem-ph/9602003

Scientific paper

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 behaviour predicted by the diffusion-collision model of Karplus and Weaver. The phenomenology of the pathways is consistent with experimental results.

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