Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all‐atom molecular dynamics simulations with ϕ value restraints

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Abstract
Delineation of the structural properties of transition states is key to deriving models for protein folding. Here we describe the structures of the transition states of the bacterial immunity proteins Im7 and Im9 obtained by all‐atom molecular dynamics simulations with ϕ value restraints derived from protein engineering experiments. This pair of proteins is of special interest because, at pH 7 and 10 °C, Im7 folds via an intermediate while Im9 folds with a two‐state transition. The structures of the transition states for Im7 and Im9, together with their radii of gyration and distances from the native state, are similar. The typical distance between any two members of the transition state ensemble of both proteins is large, with that of Im9 nearly twice that of Im7. Thus, a broad range of structures make up the transition state ensembles of these proteins. The ensembles satisfy the set of rather low ϕ values and yet are consistent with high βT values (> 0.85 for both proteins). For both Im7 and Im9 the inter‐helical angles are highly variable in the transition state ensembles, although the native contacts between helices I and IV are well conserved. By measuring the distribution of the accessible surface area for each residue we show that the hydrophobic residues that are buried in the native state remain buried in the transition state, corresponding to a hydrophobic collapse to a relatively ordered globule. The data provide new insights into the structural properties of the transition states of these proteins at an atomic level of detail and show that molecular dynamics simulations with ϕ value restraints can significantly enhance the knowledge of the transition state ensembles (TSE) provided by the experimental ϕ values alone. Proteins 2004;54:000–000.