Three key residues form a critical contact network in a protein folding transition state.
Determining how a protein folds is a central problem in structural biology. The rate of folding of many proteins is determined by the transition state, so that a knowledge of its structure is essential for understanding the protein folding reaction. Here we use mutation measurements--which determine the role of individual residues in stabilizing the transition state--as restraints in a Monte Carlo sampling procedure to determine the ensemble of structures that make up the transition state. We apply this approach to the experimental data for the 98-residue protein acylphosphatase, and obtain a transition-state ensemble with the native-state topology and an average root-mean-square deviation of 6 A from the native structure. Although about 20 residues with small positional fluctuations form the structural core of this transition state, the native-like contact network of only three of these residues is sufficient to determine the overall fold of the protein. This result reveals how a nucleation mechanism involving a small number of key residues can lead to folding of a polypeptide chain to its unique native-state structure.
Vendruscolo
M
M
Oxford Centre for Molecular Sciences, New Chemistry Laboratory, University of Oxford, UK.
Paci
E
E
Dobson
C M
CM
Karplus
M
M
D017766:Acid Anhydride Hydrolases / Q000737:chemistry* / Q000235:genetics; D001665:Binding Sites; D008958:Models, Molecular; D009010:Monte Carlo Method; D009154:Mutation; D011487:Protein Conformation; D017510:Protein Folding; D000097024:Acylphosphatase
D017766:Acid Anhydride Hydrolases; D000097024:Acylphosphatase