1997/06/11 by D. Hoffmann, Hoffmann, D., E. W. Knapp +1
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · #Biological Physics (physics.bio-ph) #Chemical Physics (physics.chem-ph) #FOS: Biological sciences #FOS: Physical sciences #Quantitative Biology (q-bio) #Soft Condensed Matter (cond-mat.soft) #cond-mat.soft #physics.bio-ph #physics.chem-ph #q-bio
paper · pdf · doi:10.48550/arxiv.physics/9706018
24 pages, LaTeX, 6 figures, to appear in J. Phys. Chem., see also chem-ph/9602003
arxiv created 1997/06/11 · arxiv updated 2009/11/30
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.