Effects of Zinc Binding on the Structure and Dynamics of the Intrinsically Disordered Protein Prothymosin α:  Evidence for Metalation as an Entropic Switch

Abstract

Prothymosin alpha (ProTalpha) is a small acidic protein that is highly conserved among mammals. The human form has 110 amino acid residues (M.W. 12.1 kDa; pI approximately 3.5) and is found to be expressed in a wide variety of tissues. ProTalpha plays an essential role in cell proliferation and apoptosis, and it is involved in transcriptional regulation of oxidative stress-protecting genes. Despite the multiple biological functions ProTalpha has, the protein does not adopt a well-defined three-dimensional structure under physiological conditions. Previous studies have shown that the interaction between ProTalpha and some of its protein targets is significantly enhanced in the presence of zinc ions, suggesting that zinc binding plays a crucial role in the protein's function. In this work, we use nuclear magnetic resonance spectroscopy and electrospray ionization mass spectrometry to characterize the structure and dynamics of ProTalpha and its complexation with Zn2+. We found that zinc binding causes partial folding of the C-terminal half of ProTalpha, especially the Glu-rich region, while the N-terminal portion of the protein remains largely unstructured. The metalated protein also exhibits a significantly reduced flexibility. ProTalpha shows a high specificity for Zn2+, and the interactions with other divalent cations (Ca2+, Mg2+) are much weaker. On the basis of the site-specific information obtained here, as well as the results from previous studies, we propose that the conformational and dynamic changes upon zinc binding may act as an entropic switch that greatly facilitates the binding to other proteins.

Microsecond Molecular Dynamics Simulations of Intrinsically Disordered Proteins Involved in the Oxidative Stress Response

“…The contact plots and structures from the MD simulations show that the β-turns formed by ProTα and Neh2 at their Keap1-binding sites stretched out in both directions to form antiparallel β-sheets (Figure 6). This finding was in good agreement with previous NMR results, which suggest that residual structures may exist in regions surrounding the Keap1-binding motifs of disordered ProTα and Neh2 [46], [78]. Interestingly, Neh2 has relatively higher 1 H- 15 N heteronuclear NOE values in its Keap1-binding region, indicating a less dynamic free-state [46].…”

Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides

“…63 In all, therefore, eight IDPs were selected for simulation; these were the amyloid β (1–40) peptide (Aβ (1–40) ), 64 suppressor of Mec1 lethality (Sml1), 65 Lotus japonicas IDP 1 ( Lj IDP1), 66 prothymosin α (ProTα), 67 abscisic acid stress ripening 1 (ASR1), 68 the nucleoporin Nup116, 69 α-Synuclein (α-Syn) 70 and the cystic fibrosis transmembrane conductance regulator regulatory region (CFTR R). 71 …”

Physicochemical Properties of Cells and Their Effects on Intrinsically Disordered Proteins (IDPs)

“…Zn 2+ binding to ProThymosin α (ProTα) increases transient helicity from <1% to 12% 59,60 and induces partial folding of its C-terminal Glu-rich region. 60 Metal binding can also promote oligomerization. In the case of HIV-1 integrase, the Zn 2+ -bound protein tetramerizes readily.…”