Quantifying the structural requirements of the folding transition state of protein A and other systems

The B-domain of protein A is a small three-helix bundle that has been the subject of considerable experimental and theoretical investigation. Nevertheless, a unified view of the structure of the transition-state ensemble (TSE) is still lacking. To characterize the TSE of this surprisingly challenging protein, we apply a combination of psi analysis (which probes the role of specific side-chain to side-chain contacts) and kinetic H/D amide isotope effects (which measures hydrogen-bond content), building upon previous studies using mutational phi analysis (which probes the energetic influence of side-chain substitutions). The second helix is folded in the TSE, while helix formation appears just at the carboxy and amino termini of the first and third helices, respectively. The experimental data suggest a homogenous yet plastic TS with a native-like topology. This study generalizes our earlier conclusion, based on two larger alpha/beta proteins, that the TSEs of most small proteins achieve approximately 70% of their native state's relative contact order. This high percentage limits the degree of possible TS heterogeneity and requires a reevaluation of the structural content of the TSE of other proteins, especially when they are characterized as small or polarized.