Pathway heterogeneity in protein folding

We generate ab initio folding pathways in two single‐domain proteins, hyperthermophile variant of protein G domain (1gb4) and ubiquitin (1ubi ), both presumed to be two‐state folders . Both proteins are endowed with the same topology but, as shown in this work, rely to a different extent on large‐scale context to find their native folds. First, we demonstrate a generic feature of two‐state folders: A downsizing of structural fluctuations is achieved only when the protein reaches a stationary plateau maximizing the number of highly protected hydrogen bonds. This enables us to identify the folding nucleus and show that folding does not become expeditious until a topology is generated that is able to protect intramolecular hydrogen bonds from water attack. Pathway heterogeneity is shown to be dependent on the extent to which the protein relies on large‐scale context to fold, rather than on contact order: Proteins that can only stabilize native secondary structure by packing it against scaffolding hydrophobic moieties are meant to have a heterogeneous transition‐state ensemble if they are to become successful folders (otherwise, successful folding would be too fortuitous an event.) We estimate mutational Φ values as ensemble averages and deconvolute individual‐route contributions to the averaged two‐state kinetic picture. Our results find experimental corroboration in the well‐studied chymotrypsin inhibitor (CI2), while leading to verifiable predictions for the other two study cases. Proteins 2002;48:293–310. © 2002 Wiley‐Liss, Inc.