Identification of Rare Partially Unfolded States in Equilibrium with the Native Conformation in an All β-Barrel Protein

Abstract Human acidic fibroblast growth factor 1 (hFGF-1) is an all β-barrel protein, and the secondary structural elements in the protein include 12 antiparallel β-strands arranged into a β-trefoil fold. In the present study, we investigate the stability of hFGF-1 by hydrogen-deuterium exchange as a function of urea concentration. Urea-induced equilibrium unfolding of hFGF-1 monitored by fluorescence and CD spectroscopy suggests that the protein unfolds by a two-state (native to denatured) mechanism. Hydrogen exchange in hFGF-1, under the experimental conditions used, occurs by the EX2 mechanism. In contrast to the equilibrium unfolding events monitored by optical probes, native state hydrogen exchange data show that the β-trefoil architecture of hFGF-1 does not behave as a single cooperative unit. There are at least two structurally independent units with differing stabilities in hFGF-1. β-Strands I, II, III, VI, VII, X, XI, and XII fit into the global unfolding isotherm. By contrast, residues in β-strands IV, V, VIII, and IX exchange by the subfolding isotherm and could be responsible for the occurrence of high-energy partially unfolded state(s) in hFGF-1. There appears to be a broad continuum of stabilities among the four β-strands (β-strands IV, V, VIII, and IX) constituting the subglobal folding unit. The slow exchanging residues in hFGF-1 do not represent the folding nucleus of the protein.