In silico folding of a three helix protein and characterization of its free-energy landscape in an all-atom force field.
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 A 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.
Herges
T
T
Forschungszentrum Karlsruhe, Institut für Nanotechnologie, 76021 Karlsruhe, Germany.
Wenzel
W
W
D000595:Amino Acid Sequence; D003198:Computer Simulation; D004735:Energy Transfer; D006678:HIV / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D013314:Stress, Mechanical; D013329:Structure-Activity Relationship; D014764:Viral Proteins / Q000032:analysis / Q000737:chemistry*
D014764:Viral Proteins