In Silico Folding of a Three Helix Protein and Characterization of Its Free-Energy Landscape in an All-Atom Force Field

T. Herges and W. Wenzel
Phys. Rev. Lett. 94, 018101 – Published 5 January 2005

Abstract

We report the reproducible first-principles folding of the 40 amino-acid, three-helix headpiece of the HIV accessory protein in a recently developed all-atom free-energy force field. Six of 20 simulations using an adapted basin-hopping method converged to better than 3 Å backbone rms deviation to the experimental structure. Using over 60 000 low-energy conformations of this protein, we constructed a decoy tree that completely characterizes its folding funnel.

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  • Received 29 October 2003

DOI:https://doi.org/10.1103/PhysRevLett.94.018101

©2005 American Physical Society

Authors & Affiliations

T. Herges and W. Wenzel*

  • Forschungszentrum Karlsruhe, Institut für Nanotechnologie, 76021 Karlsruhe, Germany

  • *Electronic address: wenzel@int.fzk.de

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Vol. 94, Iss. 1 — 14 January 2005

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