Prediction of quaternary structure of coiled coils. Application to mutants of the GCN4 leucine zipper.
Using a simplified protein model, the equilibrium between different oligomeric species of the wild-type GCN4 leucine zipper and seven of its mutants have been predicted. Over the entire experimental concentration range, agreement with experiment is found in five cases, while in two cases agreement is found over a portion of the concentration range. These studies demonstrate a methodology for predicting coiled coil quaternary structure and allow for the dissection of the interactions responsible for the global fold. In agreement with the conclusion of Harbury et al., the results of the simulations indicate that the pattern of hydrophobic and hydrophilic residues alone is insufficient to define a protein's three-dimensional structure. In addition, these simulations indicate 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, Scripps Research Institute, La Jolla, CA 92037, USA.
Kolinski
A
A
Brooks
C L
CL
Skolnick
J
J
D003198:Computer Simulation; D004268:DNA-Binding Proteins; D005656:Fungal Proteins / Q000737:chemistry*; D006860:Hydrogen Bonding; D016350:Leucine Zippers; D009010:Monte Carlo Method; D009154:Mutation; D011487:Protein Conformation; D017510:Protein Folding; D011494:Protein Kinases / Q000737:chemistry*; D029701:Saccharomyces cerevisiae Proteins; D013816:Thermodynamics
D004268:DNA-Binding Proteins; D005656:Fungal Proteins; D029701:Saccharomyces cerevisiae Proteins; D011494:Protein Kinases