Prediction of the folding pathways and structure of the GCN4 leucine zipper.
A hierarchical approach is described for the prediction of the three-dimensional structure and folding pathway of the GCN4 leucine zipper. Dimer assembly is simulated by Monte Carlo dynamics. The resulting lowest energy structures undergo cooperative rearrangement of their hydrophobic core leading to side-chain fixation. The coarse-grained structures are further refined using a molecular dynamics annealing protocol. This produces full atom models with a backbone root-mean-square deviation from the crystal structure of 0.81 A. Thus, we demonstrate the predictive ability of our approach to yield high resolution structures of small coiled coils from their sequence.
Vieth
M
M
Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037.
Kolinski
A
A
Brooks
C L
CL
Skolnick
J
J
D000595:Amino Acid Sequence; D018360:Crystallography, X-Ray; D004268:DNA-Binding Proteins / Q000737:chemistry; D005656:Fungal Proteins / Q000737:chemistry* / Q000378:metabolism; D016350:Leucine Zippers; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D017510:Protein Folding; D011494:Protein Kinases / Q000737:chemistry* / Q000378:metabolism; D017433:Protein Structure, Secondary; D029701:Saccharomyces cerevisiae Proteins
D004268:DNA-Binding Proteins; D005656:Fungal Proteins; D029701:Saccharomyces cerevisiae Proteins; D011494:Protein Kinases