Experimental support for the foldability–function tradeoff hypothesis: Segregation of the folding nucleus and functional regions in fibroblast growth factor‐1

Abstract

The acquisition of function is often associated with destabilizing mutations, giving rise to the stability-function tradeoff hypothesis. To test whether function is also accommodated at the expense of foldability, fibroblast growth factor-1 (FGF-1) was subjected to a comprehensive u-value analysis at each of the 11 turn regions. FGF-1, a b-trefoil fold, represents an excellent model system with which to evaluate the influence of function on foldability: because of its threefold symmetric structure, analysis of FGF-1 allows for direct comparisons between symmetryrelated regions of the protein that are associated with function to those that are not; thus, a structural basis for regions of foldability can potentially be identified. The resulting u-value distribution of FGF-1 is highly polarized, with the majority of positions described as either foldedlike or denatured-like in the folding transition state. Regions important for folding are shown to be asymmetrically distributed within the protein architecture; furthermore, regions associated with function (i.e., heparin-binding affinity and receptor-binding affinity) are localized to regions of the protein that fold after barrier crossing (late in the folding pathway). These results provide experimental support for the foldability-function tradeoff hypothesis in the evolution of FGF-1. Notably, the results identify the potential for folding redundancy in symmetric protein architecture with important implications for protein evolution and design.

Detection of Folding Sites of β-Trefoil Fold Proteins Based on Amino Acid Sequence Analyses and Structure-Based Sequence Alignment

“…In preceding studies, residues in β-strand 2 and β-strands 5-8 are protected in the early stage of folding revealed by H/D exchange experiments of NMR [17,18]. Longo et al [13][14] and Xia et al [15] reported that the folding nucleus detected by the ϕ-value analyses consists of residues 16-58 in β-strands 2-6. Figures 3 and 4 presents the ADM and the F-value plot with the results of the H/D exchange experiment for 2K8R.…”

“…simulations [20,21] for FGF-1, IL-1β and for His were performed to identify their folding mechanisms. These studies revealed the differences in overall folding pathways among these proteins, while these proteins commonly start to fold at the central β-strands [13,17].…”

“…This protein binds to heparin at the residues 105-121, called turn 11 [13,14,18]. It has been reported that this functional site folds in the late stage of the folding process (the foldability-function tradeoff hypothesis) [13,14,21].…”

“…This protein binds to heparin at the residues 105-121, called turn 11 [13,14,18]. It has been reported that this functional site folds in the late stage of the folding process (the foldability-function tradeoff hypothesis) [13,14,21]. In preceding studies, residues in β-strand 2 and β-strands 5-8 are protected in the early stage of folding revealed by H/D exchange experiments of NMR [17,18].…”

“…McLachlan [3] Murzin et al [4] Ponting et al [8] Lee et al [9,10] Broom et al [11,12] Longo et al [13,14] and Xia et al [15] pointed out that and proposed key residues in the three symmetrical units to form the β-Trefoil fold.…”