Prediction of the quaternary structure of coiled coils: GCN4 leucine zipper and its mutants.
A methodology for predicting coiled coil quaternary structure and for the dissection of the interactions responsible for the global fold is described. Application is made to the equilibrium between different oligomeric species of the wild type GCN4 leucine zipper and seven of its mutants that were studied by Harbury et al. Over the entire experimental concentration range, agreement with experiment is found in five cases, while in two other cases, agreement is found over a portion of the concentration range. These simulations suggest that the degree of chain association is determined by the balance between specific side chain packing preferences and the entropy reduction associated with side chain burial in higher order multimers.
Vieth
M
M
Department of Molecular Biology and Chemistry, Scripps Research Institute, La Jolla, California 92037, USA.
Kolinski
A
A
Brooks
C L
CL
Skolnick
J
J
D019943:Amino Acid Substitution; D003198:Computer Simulation; D004268:DNA-Binding Proteins / Q000737:chemistry; D004355:Drug Stability; D019277:Entropy; D005656:Fungal Proteins / Q000737:chemistry*; D016350:Leucine Zippers; D008958:Models, Molecular; D016297:Mutagenesis, Site-Directed; D017354:Point Mutation; D011487:Protein Conformation; D017510:Protein Folding; D011494:Protein Kinases / Q000737:chemistry*; D017433:Protein Structure, Secondary; D015203:Reproducibility of Results; D029701:Saccharomyces cerevisiae Proteins
D004268:DNA-Binding Proteins; D005656:Fungal Proteins; D029701:Saccharomyces cerevisiae Proteins; D011494:Protein Kinases